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P40422 (RPAB4_YEAST) Reviewed, UniProtKB/Swiss-Prot

Last modified June 11, 2014. Version 141. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (4) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
DNA-directed RNA polymerases I, II, and III subunit RPABC4

Short name=RNA polymerases I, II, and III subunit ABC4
Alternative name(s):
ABC10-alpha
Gene names
Name:RPC10
Synonyms:RPB12
Ordered Locus Names:YHR143W-A
ORF Names:YHR143BW
OrganismSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]
Taxonomic identifier559292 [NCBI]
Taxonomic lineageEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces

Protein attributes

Sequence length70 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

DNA-dependent RNA polymerases catalyze the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common component of RNA polymerases I, II and III which synthesize ribosomal RNA precursors, mRNA precursors and many functional non-coding RNAs, and a small RNAs, such as 5S rRNA and tRNAs, respectively. RNA polymerases are composed of mobile elements that move relative to each other. In Pol II, the core element with the central large cleft comprises RPB3, RBP10, RPB11, RPB12 and regions of RPB1 and RPB2 forming the active center. Ref.23 Ref.24 Ref.25

Subunit structure

Component of the RNA polymerase I (Pol I), RNA polymerase II (Pol II) and RNA polymerase III (Pol III) complexes. Component of the RNA polymerase I (Pol I) complex consisting of 14 subunits: RPA135, RPA190, RPC40, RPA14, RPB5, RPO26, RPA43, RPB8, RPA12, RPB10, RPC19, RPC10, RPA49 and RPA34. The complex is composed of a horseshoe-shaped core containing ten subunits (RPA135, RPA190, RPB5, RPO26, RPB8, RPB10, RPC10, RPA12, RPC19 and RPC40) where RPA135 and RPA190 form the DNA-binding cleft. Outside of the core, RPA14 and RPA43 form the stalk that mediates interactions with transcription initiation factors and newly synthesized RNA. Component of the RNA polymerase II (Pol II) complex consisting of 12 subunits: RPO21, RPB2, RPB3, RPB4, RPB5, RPO26, RPB7, RPB8, RPB9, RPB10 and RPC10. Component of the RNA polymerase III (Pol III) complex consisting of 17 subunits. Interacts, via its C-terminus, with TFIIIC subunit TFC4. Ref.6 Ref.23 Ref.24 Ref.25

Subcellular location

Nucleusnucleolus Ref.7.

Post-translational modification

The N-terminus is blocked.

Miscellaneous

Present with 907 molecules/cell in log phase SD medium.

Sequence similarities

Belongs to the archaeal RpoP/eukaryotic RPC10 RNA polymerase subunit family.

Ontologies

Keywords
   Biological processRibosome biogenesis
Transcription
   Cellular componentDNA-directed RNA polymerase
Nucleus
   DomainZinc-finger
   LigandMetal-binding
Zinc
   Technical term3D-structure
Complete proteome
Direct protein sequencing
Reference proteome
Gene Ontology (GO)
   Biological_processribosome biogenesis

Inferred from electronic annotation. Source: UniProtKB-KW

tRNA transcription from RNA polymerase III promoter

Inferred from direct assay PubMed 3905793. Source: SGD

transcription from RNA polymerase I promoter

Inferred from direct assay Ref.24. Source: UniProtKB

transcription from RNA polymerase II promoter

Inferred from mutant phenotype PubMed 10531351. Source: SGD

transcription from RNA polymerase III promoter

Inferred from mutant phenotype PubMed 10531351. Source: SGD

transcription, RNA-templated

Inferred from direct assay PubMed 18004386. Source: GOC

   Cellular_componentDNA-directed RNA polymerase I complex

Inferred from direct assay Ref.24. Source: UniProtKB

DNA-directed RNA polymerase II, core complex

Inferred from direct assay PubMed 1331084PubMed 1748681. Source: SGD

DNA-directed RNA polymerase III complex

Inferred from direct assay PubMed 10611227PubMed 1748681PubMed 3905793. Source: SGD

nucleoplasm

Traceable author statement. Source: Reactome

   Molecular_functionDNA binding

Inferred from electronic annotation. Source: InterPro

RNA polymerase I activity

Inferred from direct assay Ref.24. Source: UniProtKB

zinc ion binding

Inferred from direct assay PubMed 1748681. Source: SGD

Complete GO annotation...

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 7070DNA-directed RNA polymerases I, II, and III subunit RPABC4
PRO_0000159753

Regions

Zinc finger31 – 5121C4-type

Sites

Metal binding311Zinc
Metal binding341Zinc
Metal binding481Zinc
Metal binding511Zinc

Secondary structure

............... 70
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P40422 [UniParc].

Last modified February 1, 1995. Version 1.
Checksum: 066A3D982EC7361E

FASTA707,716
        10         20         30         40         50         60 
MSREGFQIPT NLDAAAAGTS QARTATLKYI CAECSSKLSL SRTDAVRCKD CGHRILLKAR 

        70 
TKRLVQFEAR 

« Hide

References

« Hide 'large scale' references
[1]"RPC10 encodes a new mini subunit shared by yeast nuclear RNA polymerases."
Treich I., Carles C., Riva M., Sentenac A.
Gene Expr. 2:31-37(1992) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 4-23 AND 64-70.
Strain: ATCC 204508 / S288c.
[2]"Complete nucleotide sequence of Saccharomyces cerevisiae chromosome VIII."
Johnston M., Andrews S., Brinkman R., Cooper J., Ding H., Dover J., Du Z., Favello A., Fulton L., Gattung S., Geisel C., Kirsten J., Kucaba T., Hillier L.W., Jier M., Johnston L., Langston Y., Latreille P. expand/collapse author list , Louis E.J., Macri C., Mardis E., Menezes S., Mouser L., Nhan M., Rifkin L., Riles L., St Peter H., Trevaskis E., Vaughan K., Vignati D., Wilcox L., Wohldman P., Waterston R., Wilson R., Vaudin M.
Science 265:2077-2082(1994) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: ATCC 204508 / S288c.
[3]"The reference genome sequence of Saccharomyces cerevisiae: Then and now."
Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R., Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S., Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M., Cherry J.M.
G3 (Bethesda) 4:389-398(2014) [PubMed] [Europe PMC] [Abstract]
Cited for: GENOME REANNOTATION.
Strain: ATCC 204508 / S288c.
[4]"Approaching a complete repository of sequence-verified protein-encoding clones for Saccharomyces cerevisiae."
Hu Y., Rolfs A., Bhullar B., Murthy T.V.S., Zhu C., Berger M.F., Camargo A.A., Kelley F., McCarron S., Jepson D., Richardson A., Raphael J., Moreira D., Taycher E., Zuo D., Mohr S., Kane M.F., Williamson J. expand/collapse author list , Simpson A.J.G., Bulyk M.L., Harlow E., Marsischky G., Kolodner R.D., LaBaer J.
Genome Res. 17:536-543(2007) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
Strain: ATCC 204508 / S288c.
[5]"The yeast RNA polymerase III transcription machinery: a paradigm for eukaryotic gene activation."
Chedin S., Ferri M.L., Peyroche G., Andrau J.-C., Jourdain S., Lefebvre O., Werner M., Carles C., Sentenac A.
Cold Spring Harb. Symp. Quant. Biol. 63:381-389(1998) [PubMed] [Europe PMC] [Abstract]
Cited for: REVIEW ON THE RNA POL III COMPLEX.
[6]"Interaction between yeast RNA polymerase III and transcription factor TFIIIC via ABC10alpha and tau131 subunits."
Dumay H., Rubbi L., Sentenac A., Marck C.
J. Biol. Chem. 274:33462-33468(1999) [PubMed] [Europe PMC] [Abstract]
Cited for: INTERACTION WITH TFC4.
[7]"Global analysis of protein localization in budding yeast."
Huh W.-K., Falvo J.V., Gerke L.C., Carroll A.S., Howson R.W., Weissman J.S., O'Shea E.K.
Nature 425:686-691(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
[8]"Global analysis of protein expression in yeast."
Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N., O'Shea E.K., Weissman J.S.
Nature 425:737-741(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
[9]"Structural basis of transcription: RNA polymerase II at 2.8 A resolution."
Cramer P., Bushnell D.A., Kornberg R.D.
Science 292:1863-1876(2001) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS) OF THE RNA POL II CORE COMPLEX.
[10]"Structural basis of transcription: an RNA polymerase II elongation complex at 3.3 A resolution."
Gnatt A.L., Cramer P., Fu J., Bushnell D.A., Kornberg R.D.
Science 292:1876-1882(2001) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (3.3 ANGSTROMS) OF THE RNA POL II CORE COMPLEX.
[11]"Structural basis of transcription: alpha-amanitin-RNA polymerase II cocrystal at 2.8 A resolution."
Bushnell D.A., Cramer P., Kornberg R.D.
Proc. Natl. Acad. Sci. U.S.A. 99:1218-1222(2002) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS) OF THE RNA POL II CORE COMPLEX IN COMPLEX WITH ALPHA-AMANITIN.
[12]"Architecture of the RNA polymerase II-TFIIS complex and implications for mRNA cleavage."
Kettenberger H., Armache K.J., Cramer P.
Cell 114:347-357(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (3.8 ANGSTROMS) OF THE RNA POL II COMPLEX IN COMPLEX WITH DST1.
[13]"RNA polymerase II/TFIIF structure and conserved organization of the initiation complex."
Chung W.H., Craighead J.L., Chang W.H., Ezeokonkwo C., Bareket-Samish A., Kornberg R.D., Asturias F.J.
Mol. Cell 12:1003-1013(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: ELECTRON MICROSCOPY OF THE RNA POL II/TFIIF COMPLEX.
[14]"Architecture of initiation-competent 12-subunit RNA polymerase II."
Armache K.J., Kettenberger H., Cramer P.
Proc. Natl. Acad. Sci. U.S.A. 100:6964-6968(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (4.2 ANGSTROMS) OF THE RNA POL II COMPLEX.
[15]"Complete, 12-subunit RNA polymerase II at 4.1-A resolution: implications for the initiation of transcription."
Bushnell D.A., Kornberg R.D.
Proc. Natl. Acad. Sci. U.S.A. 100:6969-6973(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (4.1 ANGSTROMS) OF THE RNA POL II CORE COMPLEX.
[16]"Structural basis of transcription: nucleotide selection by rotation in the RNA polymerase II active center."
Westover K.D., Bushnell D.A., Kornberg R.D.
Cell 119:481-489(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) OF THE RNA POL II CORE COMPLEX.
[17]"Complete RNA polymerase II elongation complex structure and its interactions with NTP and TFIIS."
Kettenberger H., Armache K.J., Cramer P.
Mol. Cell 16:955-965(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (4.5 ANGSTROMS).
[18]"Structural basis of transcription: an RNA polymerase II-TFIIB cocrystal at 4.5 Angstroms."
Bushnell D.A., Westover K.D., Davis R.E., Kornberg R.D.
Science 303:983-988(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (4.5 ANGSTROMS) OF THE RNA POL II CORE COMPLEX.
[19]"Structures of complete RNA polymerase II and its subcomplex, Rpb4/7."
Armache K.J., Mitterweger S., Meinhart A., Cramer P.
J. Biol. Chem. 280:7131-7134(2005) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (3.8 ANGSTROMS) OF THE RNA POL II COMPLEX.
[20]"Structural biology of RNA polymerase III: subcomplex C17/25 X-ray structure and 11 subunit enzyme model."
Jasiak A.J., Armache K.J., Martens B., Jansen R.P., Cramer P.
Mol. Cell 23:71-81(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: 3D-STRUCTURE MODELING OF THE POL III CORE COMPLEX.
[21]"Structure of an RNA polymerase II-RNA inhibitor complex elucidates transcription regulation by noncoding RNAs."
Kettenberger H., Eisenfuhr A., Brueckner F., Theis M., Famulok M., Cramer P.
Nat. Struct. Mol. Biol. 13:44-48(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (3.8 ANGSTROMS) OF THE RNA POL II COMPLEX IN COMPLEX WITH INHIBITING NON-CODING RNA.
[22]"Phasing RNA polymerase II using intrinsically bound Zn atoms: an updated structural model."
Meyer P.A., Ye P., Zhang M., Suh M.H., Fu J.
Structure 14:973-982(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (4.15 ANGSTROMS) OF THE RNA POL II COMPLEX.
[23]"Functional architecture of RNA polymerase I."
Kuhn C.D., Geiger S.R., Baumli S., Gartmann M., Gerber J., Jennebach S., Mielke T., Tschochner H., Beckmann R., Cramer P.
Cell 131:1260-1272(2007) [PubMed] [Europe PMC] [Abstract]
Cited for: STRUCTURE BY ELECTRON MICROSCOPY (12.00 ANGSTROMS) OF THE POL I COMPLEX, FUNCTION, SUBUNIT.
[24]"Crystal structure of the 14-subunit RNA polymerase I."
Fernandez-Tornero C., Moreno-Morcillo M., Rashid U.J., Taylor N.M., Ruiz F.M., Gruene T., Legrand P., Steuerwald U., Muller C.W.
Nature 502:644-649(2013) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS) OF THE POL I COMPLEX, FUNCTION, SUBUNIT.
[25]"RNA polymerase I structure and transcription regulation."
Engel C., Sainsbury S., Cheung A.C., Kostrewa D., Cramer P.
Nature 502:650-655(2013) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS) OF THE POL I COMPLEX, FUNCTION, SUBUNIT.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
U23378 Genomic DNA. Translation: AAA64417.1.
U10397 Genomic DNA. Translation: AAB68994.1.
AY558549 Genomic DNA. Translation: AAS56875.1.
BK006934 Genomic DNA. Translation: DAA06837.1.
PIRS58932.
RefSeqNP_012013.1. NM_001179273.1.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1I3QX-ray3.10L1-70[»]
1I50X-ray2.80L1-70[»]
1I6HX-ray3.30L1-70[»]
1K83X-ray2.80L1-70[»]
1NIKX-ray4.10L1-70[»]
1NT9X-ray4.20L1-70[»]
1PQVX-ray3.80L1-70[»]
1R5UX-ray4.50L1-70[»]
1R9SX-ray4.25L1-70[»]
1R9TX-ray3.50L1-70[»]
1SFOX-ray3.61L1-70[»]
1TWAX-ray3.20L1-70[»]
1TWCX-ray3.00L1-70[»]
1TWFX-ray2.30L1-70[»]
1TWGX-ray3.30L1-70[»]
1TWHX-ray3.40L1-70[»]
1WCMX-ray3.80L1-70[»]
1Y1VX-ray3.80L1-70[»]
1Y1WX-ray4.00L1-70[»]
1Y1YX-ray4.00L1-70[»]
1Y77X-ray4.50L1-70[»]
2B63X-ray3.80L1-70[»]
2B8KX-ray4.15L1-70[»]
2E2HX-ray3.95L1-70[»]
2E2IX-ray3.41L1-70[»]
2E2JX-ray3.50L1-70[»]
2JA5X-ray3.80L1-70[»]
2JA6X-ray4.00L1-70[»]
2JA7X-ray3.80L/X1-70[»]
2JA8X-ray3.80L1-70[»]
2NVQX-ray2.90L1-70[»]
2NVTX-ray3.36L1-70[»]
2NVXX-ray3.60L1-70[»]
2NVYX-ray3.40L1-70[»]
2NVZX-ray4.30L1-70[»]
2R7ZX-ray3.80L1-70[»]
2R92X-ray3.80L1-70[»]
2R93X-ray4.00L1-70[»]
2VUMX-ray3.40L1-70[»]
2YU9X-ray3.40L1-70[»]
3CQZX-ray2.80L1-70[»]
3FKIX-ray3.88L1-70[»]
3GTGX-ray3.78L1-70[»]
3GTJX-ray3.42L1-70[»]
3GTKX-ray3.80L1-70[»]
3GTLX-ray3.38L1-70[»]
3GTMX-ray3.80L1-70[»]
3GTOX-ray4.00L1-70[»]
3GTPX-ray3.90L1-70[»]
3GTQX-ray3.80L1-70[»]
3H3VX-ray4.00M1-70[»]
3HOUX-ray3.20L/X1-70[»]
3HOVX-ray3.50L1-70[»]
3HOWX-ray3.60L1-70[»]
3HOXX-ray3.65L1-70[»]
3HOYX-ray3.40L1-70[»]
3HOZX-ray3.65L1-70[»]
3I4MX-ray3.70L1-70[»]
3I4NX-ray3.90L1-70[»]
3J1Nelectron microscopy16.00L1-70[»]
3K1FX-ray4.30L1-70[»]
3K7AX-ray3.80L1-70[»]
3M3YX-ray3.18L1-70[»]
3M4OX-ray3.57L1-70[»]
3PO2X-ray3.30L1-70[»]
3PO3X-ray3.30L1-70[»]
3QT1X-ray4.30L1-70[»]
3RZDX-ray3.30L1-70[»]
3RZOX-ray3.00L1-70[»]
3S14X-ray2.85L1-70[»]
3S15X-ray3.30L1-70[»]
3S16X-ray3.24L1-70[»]
3S17X-ray3.20L1-70[»]
3S1MX-ray3.13L1-70[»]
3S1NX-ray3.10L1-70[»]
3S1QX-ray3.30L1-70[»]
3S1RX-ray3.20L1-70[»]
3S2DX-ray3.20L1-70[»]
3S2HX-ray3.30L1-70[»]
4A3BX-ray3.50L1-70[»]
4A3CX-ray3.50L1-70[»]
4A3DX-ray3.40L1-70[»]
4A3EX-ray3.40L1-70[»]
4A3FX-ray3.50L1-70[»]
4A3GX-ray3.50L1-70[»]
4A3IX-ray3.80L1-70[»]
4A3JX-ray3.70L1-70[»]
4A3KX-ray3.50L1-70[»]
4A3LX-ray3.50L1-70[»]
4A3MX-ray3.90L1-70[»]
4A93X-ray3.40L1-70[»]
4BBRX-ray3.40L1-70[»]
4BBSX-ray3.60L1-70[»]
4BXXX-ray3.28L1-70[»]
4BXZX-ray4.80L1-70[»]
4BY1X-ray3.60L1-70[»]
4BY7X-ray3.15L1-70[»]
4C2MX-ray2.801/L1-70[»]
4C3HX-ray3.27L1-70[»]
4C3IX-ray3.0L1-70[»]
4C3JX-ray3.35L1-70[»]
ProteinModelPortalP40422.
SMRP40422. Positions 25-70.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid36577. 64 interactions.
DIPDIP-936N.
IntActP40422. 7 interactions.
MINTMINT-559375.
STRING4932.YHR143W-A.

Proteomic databases

MaxQBP40422.
PaxDbP40422.
PeptideAtlasP40422.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblFungiYHR143W-A; YHR143W-A; YHR143W-A.
GeneID856547.
KEGGsce:YHR143W-A.

Organism-specific databases

CYGDYHR143w-a.
SGDS000001185. RPC10.

Phylogenomic databases

eggNOGCOG1996.
HOGENOMHOG000191755.
KOK03009.
OMAKPRYSNT.
OrthoDBEOG7K0ZRP.

Enzyme and pathway databases

BioCycYEAST:G3O-31179-MONOMER.

Gene expression databases

GenevestigatorP40422.

Family and domain databases

Gene3D2.20.28.30. 1 hit.
InterProIPR006591. RNAP_P/RPABC4.
IPR029040. RPABC4/Spt4.
[Graphical view]
PfamPF03604. DNA_RNApol_7kD. 1 hit.
[Graphical view]
SMARTSM00659. RPOLCX. 1 hit.
[Graphical view]
SUPFAMSSF63393. SSF63393. 1 hit.
ProtoNetSearch...

Other

EvolutionaryTraceP40422.
NextBio982349.
PROP40422.

Entry information

Entry nameRPAB4_YEAST
AccessionPrimary (citable) accession number: P40422
Secondary accession number(s): D3DL93
Entry history
Integrated into UniProtKB/Swiss-Prot: February 1, 1995
Last sequence update: February 1, 1995
Last modified: June 11, 2014
This is version 141 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Relevant documents

Yeast chromosome VIII

Yeast (Saccharomyces cerevisiae) chromosome VIII: entries and gene names

Yeast

Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references