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Protein

Nucleoporin NDC1

Gene

NDC1

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Component of the nuclear pore complex (NPC), which plays a key role in de novo assembly and insertion of NPC in the nuclear envelope. Required for NPC and nuclear envelope assembly, possibly by forming a link between the nuclear envelope membrane and soluble nucleoporins, thereby anchoring the NPC in the membrane.2 Publications

GO - Molecular functioni

  • structural constituent of nuclear pore Source: UniProtKB

GO - Biological processi

Complete GO annotation...

Keywords - Biological processi

mRNA transport, Protein transport, Translocation, Transport

Enzyme and pathway databases

BioCyciZFISH:ENSG00000058804-MONOMER.
ReactomeiR-HSA-1169408. ISG15 antiviral mechanism.
R-HSA-159227. Transport of the SLBP independent Mature mRNA.
R-HSA-159230. Transport of the SLBP Dependant Mature mRNA.
R-HSA-159231. Transport of Mature mRNA Derived from an Intronless Transcript.
R-HSA-159236. Transport of Mature mRNA derived from an Intron-Containing Transcript.
R-HSA-165054. Rev-mediated nuclear export of HIV RNA.
R-HSA-168271. Transport of Ribonucleoproteins into the Host Nucleus.
R-HSA-168276. NS1 Mediated Effects on Host Pathways.
R-HSA-168325. Viral Messenger RNA Synthesis.
R-HSA-168333. NEP/NS2 Interacts with the Cellular Export Machinery.
R-HSA-170822. Regulation of Glucokinase by Glucokinase Regulatory Protein.
R-HSA-180746. Nuclear import of Rev protein.
R-HSA-180910. Vpr-mediated nuclear import of PICs.
R-HSA-191859. snRNP Assembly.
R-HSA-3108214. SUMOylation of DNA damage response and repair proteins.
R-HSA-3301854. Nuclear Pore Complex (NPC) Disassembly.
R-HSA-3371453. Regulation of HSF1-mediated heat shock response.
R-HSA-4570464. SUMOylation of RNA binding proteins.
R-HSA-4615885. SUMOylation of DNA replication proteins.
R-HSA-5578749. Transcriptional regulation by small RNAs.
R-HSA-6784531. tRNA processing in the nucleus.

Protein family/group databases

TCDBi1.I.1.1.3. the nuclear pore complex (npc) family.

Names & Taxonomyi

Protein namesi
Recommended name:
Nucleoporin NDC1
Short name:
hNDC1
Alternative name(s):
Transmembrane protein 48
Gene namesi
Name:NDC1
Synonyms:TMEM48
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 1

Organism-specific databases

HGNCiHGNC:25525. NDC1.

Subcellular locationi

Topology

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Topological domaini1 – 24CytoplasmicSequence analysisAdd BLAST24
Transmembranei25 – 45Helical; Name=1Sequence analysisAdd BLAST21
Topological domaini46 – 68Perinuclear spaceSequence analysisAdd BLAST23
Transmembranei69 – 89Helical; Name=2Sequence analysisAdd BLAST21
Topological domaini90 – 114CytoplasmicSequence analysisAdd BLAST25
Transmembranei115 – 135Helical; Name=3Sequence analysisAdd BLAST21
Topological domaini136 – 165Perinuclear spaceSequence analysisAdd BLAST30
Transmembranei166 – 186Helical; Name=4Sequence analysisAdd BLAST21
Topological domaini187 – 225CytoplasmicSequence analysisAdd BLAST39
Transmembranei226 – 246Helical; Name=5Sequence analysisAdd BLAST21
Topological domaini247 – 272Perinuclear spaceSequence analysisAdd BLAST26
Transmembranei273 – 293Helical; Name=6Sequence analysisAdd BLAST21
Topological domaini294 – 674CytoplasmicSequence analysisAdd BLAST381

GO - Cellular componenti

  • actin cytoskeleton Source: HPA
  • cytoplasm Source: Ensembl
  • integral component of membrane Source: UniProtKB-KW
  • membrane Source: UniProtKB
  • nuclear envelope Source: Reactome
  • nuclear membrane Source: HPA
  • nuclear pore Source: UniProtKB
  • nuclear pore transmembrane ring Source: GO_Central
  • plasma membrane Source: HPA
Complete GO annotation...

Keywords - Cellular componenti

Membrane, Nuclear pore complex, Nucleus

Pathology & Biotechi

Organism-specific databases

DisGeNETi55706.
OpenTargetsiENSG00000058804.
PharmGKBiPA142670764.

Polymorphism and mutation databases

BioMutaiNDC1.
DMDMi97180263.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002352401 – 674Nucleoporin NDC1Add BLAST674

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei406PhosphoserineCombined sources1
Modified residuei414PhosphothreonineCombined sources1
Modified residuei439PhosphoserineCombined sources1
Modified residuei440PhosphothreonineCombined sources1
Modified residuei445PhosphoserineCombined sources1
Modified residuei449PhosphothreonineCombined sources1
Modified residuei471PhosphoserineCombined sources1
Modified residuei474PhosphoserineCombined sources1

Keywords - PTMi

Phosphoprotein

Proteomic databases

EPDiQ9BTX1.
MaxQBiQ9BTX1.
PaxDbiQ9BTX1.
PeptideAtlasiQ9BTX1.
PRIDEiQ9BTX1.

PTM databases

iPTMnetiQ9BTX1.
PhosphoSitePlusiQ9BTX1.
SwissPalmiQ9BTX1.

Expressioni

Gene expression databases

BgeeiENSG00000058804.
CleanExiHS_TMEM48.
GenevisibleiQ9BTX1. HS.

Organism-specific databases

HPAiHPA070882.

Interactioni

Subunit structurei

Interacts with the NUP35/NUP53 (By similarity). Interacts with AAAS, anchoring it to the nuclear envelope.By similarity1 Publication

Protein-protein interaction databases

BioGridi120831. 44 interactors.
IntActiQ9BTX1. 20 interactors.
STRINGi9606.ENSP00000360483.

Structurei

3D structure databases

ProteinModelPortaliQ9BTX1.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the NDC1 family.Curated

Keywords - Domaini

Transmembrane, Transmembrane helix

Phylogenomic databases

eggNOGiKOG4358. Eukaryota.
ENOG4110XEC. LUCA.
GeneTreeiENSGT00390000014590.
HOGENOMiHOG000231135.
HOVERGENiHBG080133.
InParanoidiQ9BTX1.
KOiK14315.
OMAiRHFKLPH.
OrthoDBiEOG091G0MME.
PhylomeDBiQ9BTX1.
TreeFamiTF324843.

Family and domain databases

InterProiIPR019049. Nucleoporin_prot_Ndc1/Nup.
[Graphical view]
PfamiPF09531. Ndc1_Nup. 1 hit.
[Graphical view]

Sequences (6)i

Sequence statusi: Complete.

This entry describes 6 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q9BTX1-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MATAVSRPCA GRSRDILWRV LGWRIVASIV WSVLFLPICT TVFIIFSRID
60 70 80 90 100
LFHPIQWLSD SFSDLYSSYV IFYFLLLSVV IIIISIFNVE FYAVVPSIPC
110 120 130 140 150
SRLALIGKII HPQQLMHSFI HAAMGMVMAW CAAVITQGQY SFLVVPCTGT
160 170 180 190 200
NSFGSPAAQT CLNEYHLFFL LTGAFMGYSY SLLYFVNNMN YLPFPIIQQY
210 220 230 240 250
KFLRFRRSLL LLVKHSCVES LFLVRNFCIL YYFLGYIPKA WISTAMNLHI
260 270 280 290 300
DEQVHRPLDT VSGLLNLSLL YHVWLCGVFL LTTWYVSWIL FKIYATEAHV
310 320 330 340 350
FPVQPPFAEG SDECLPKVLN SNPPPIIKYL ALQDLMLLSQ YSPSRRQEVF
360 370 380 390 400
SLSQPGGHPH NWTAISRECL NLLNGMTQKL ILYQEAAATN GRVSSSYPVE
410 420 430 440 450
PKKLNSPEET AFQTPKSSQM PRPSVPPLVK TSLFSSKLST PDVVSPFGTP
460 470 480 490 500
FGSSVMNRMA GIFDVNTCYG SPQSPQLIRR GPRLWTSASD QQMTEFSNPS
510 520 530 540 550
PSTSISAEGK TMRQPSVIYS WIQNKREQIK NFLSKRVLIM YFFSKHPEAS
560 570 580 590 600
IQAVFSDAQM HIWALEGLSH LVAASFTEDR FGVVQTTLPA ILNTLLTLQE
610 620 630 640 650
AVDKYFKLPH ASSKPPRISG SLVDTSYKTL RFAFRASLKT AIYRITTTFG
660 670
EHLNAVQASA EHQKRLQQFL EFKE
Length:674
Mass (Da):76,305
Last modified:May 16, 2006 - v2
Checksum:i78368FEB232895D9
GO
Isoform 2 (identifier: Q9BTX1-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     93-93: Missing.

Note: No experimental confirmation available.
Show »
Length:673
Mass (Da):76,234
Checksum:i27A688260C1B2852
GO
Isoform 3 (identifier: Q9BTX1-3) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     376-492: Missing.

Note: No experimental confirmation available.
Show »
Length:557
Mass (Da):63,572
Checksum:iC9AC3DCCCF3D5EBE
GO
Isoform 4 (identifier: Q9BTX1-4) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     509-542: GKTMRQPSVIYSWIQNKREQIKNFLSKRVLIMYF → APRGLHSGCFFRCPNAYLGIRRSVALSSSIIYRG
     543-674: Missing.

Note: No experimental confirmation available.
Show »
Length:542
Mass (Da):61,009
Checksum:i06630F6E487BAC55
GO
Isoform 5 (identifier: Q9BTX1-5) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     95-135: VPSIPCSRLALIGKIIHPQQLMHSFIHAAMGMVMAWCAAVI → I

Note: No experimental confirmation available.
Show »
Length:634
Mass (Da):71,992
Checksum:iF80C5BBAFEF9C41F
GO
Isoform 6 (identifier: Q9BTX1-6) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-115: Missing.

Note: No experimental confirmation available.
Show »
Length:559
Mass (Da):63,158
Checksum:iB2DD7D9EE6AF56EA
GO

Sequence cautioni

The sequence BAB14135 differs from that shown. Reason: Erroneous initiation.Curated
The sequence BAC03665 differs from that shown. Reason: Erroneous initiation.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti261V → A in BAG58064 (PubMed:14702039).Curated1
Sequence conflicti476Q → R in BAG58064 (PubMed:14702039).Curated1
Sequence conflicti525K → R in BAG61017 (PubMed:14702039).Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_026388154G → D.2 PublicationsCorresponds to variant rs17849721dbSNPEnsembl.1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_0553311 – 115Missing in isoform 6. 1 PublicationAdd BLAST115
Alternative sequenceiVSP_01839693Missing in isoform 2. 1 Publication1
Alternative sequenceiVSP_05533295 – 135VPSIP…CAAVI → I in isoform 5. 1 PublicationAdd BLAST41
Alternative sequenceiVSP_018397376 – 492Missing in isoform 3. 1 PublicationAdd BLAST117
Alternative sequenceiVSP_018398509 – 542GKTMR…LIMYF → APRGLHSGCFFRCPNAYLGI RRSVALSSSIIYRG in isoform 4. CuratedAdd BLAST34
Alternative sequenceiVSP_018399543 – 674Missing in isoform 4. CuratedAdd BLAST132

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
DQ141696 mRNA. Translation: AAZ73087.1.
AK001269 mRNA. Translation: BAA91592.1.
AK022618 mRNA. Translation: BAB14135.1. Different initiation.
AK091439 mRNA. Translation: BAC03665.1. Different initiation.
AK298909 mRNA. Translation: BAG61017.1.
AK295000 mRNA. Translation: BAG58064.1.
AL354612 mRNA. Translation: CAB89725.1.
AL354613 mRNA. Translation: CAB89726.1.
AL049745 Genomic DNA. Translation: CAI22180.1.
CH471059 Genomic DNA. Translation: EAX06731.1.
BC003082 mRNA. Translation: AAH03082.1.
CCDSiCCDS583.1. [Q9BTX1-1]
RefSeqiNP_001162023.1. NM_001168551.1. [Q9BTX1-5]
NP_060557.3. NM_018087.4. [Q9BTX1-1]
UniGeneiHs.476525.

Genome annotation databases

EnsembliENST00000371429; ENSP00000360483; ENSG00000058804. [Q9BTX1-1]
GeneIDi55706.
KEGGihsa:55706.
UCSCiuc001cvs.4. human. [Q9BTX1-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
DQ141696 mRNA. Translation: AAZ73087.1.
AK001269 mRNA. Translation: BAA91592.1.
AK022618 mRNA. Translation: BAB14135.1. Different initiation.
AK091439 mRNA. Translation: BAC03665.1. Different initiation.
AK298909 mRNA. Translation: BAG61017.1.
AK295000 mRNA. Translation: BAG58064.1.
AL354612 mRNA. Translation: CAB89725.1.
AL354613 mRNA. Translation: CAB89726.1.
AL049745 Genomic DNA. Translation: CAI22180.1.
CH471059 Genomic DNA. Translation: EAX06731.1.
BC003082 mRNA. Translation: AAH03082.1.
CCDSiCCDS583.1. [Q9BTX1-1]
RefSeqiNP_001162023.1. NM_001168551.1. [Q9BTX1-5]
NP_060557.3. NM_018087.4. [Q9BTX1-1]
UniGeneiHs.476525.

3D structure databases

ProteinModelPortaliQ9BTX1.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi120831. 44 interactors.
IntActiQ9BTX1. 20 interactors.
STRINGi9606.ENSP00000360483.

Protein family/group databases

TCDBi1.I.1.1.3. the nuclear pore complex (npc) family.

PTM databases

iPTMnetiQ9BTX1.
PhosphoSitePlusiQ9BTX1.
SwissPalmiQ9BTX1.

Polymorphism and mutation databases

BioMutaiNDC1.
DMDMi97180263.

Proteomic databases

EPDiQ9BTX1.
MaxQBiQ9BTX1.
PaxDbiQ9BTX1.
PeptideAtlasiQ9BTX1.
PRIDEiQ9BTX1.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000371429; ENSP00000360483; ENSG00000058804. [Q9BTX1-1]
GeneIDi55706.
KEGGihsa:55706.
UCSCiuc001cvs.4. human. [Q9BTX1-1]

Organism-specific databases

CTDi55706.
DisGeNETi55706.
GeneCardsiNDC1.
H-InvDBHIX0000603.
HGNCiHGNC:25525. NDC1.
HPAiHPA070882.
MIMi610115. gene.
neXtProtiNX_Q9BTX1.
OpenTargetsiENSG00000058804.
PharmGKBiPA142670764.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG4358. Eukaryota.
ENOG4110XEC. LUCA.
GeneTreeiENSGT00390000014590.
HOGENOMiHOG000231135.
HOVERGENiHBG080133.
InParanoidiQ9BTX1.
KOiK14315.
OMAiRHFKLPH.
OrthoDBiEOG091G0MME.
PhylomeDBiQ9BTX1.
TreeFamiTF324843.

Enzyme and pathway databases

BioCyciZFISH:ENSG00000058804-MONOMER.
ReactomeiR-HSA-1169408. ISG15 antiviral mechanism.
R-HSA-159227. Transport of the SLBP independent Mature mRNA.
R-HSA-159230. Transport of the SLBP Dependant Mature mRNA.
R-HSA-159231. Transport of Mature mRNA Derived from an Intronless Transcript.
R-HSA-159236. Transport of Mature mRNA derived from an Intron-Containing Transcript.
R-HSA-165054. Rev-mediated nuclear export of HIV RNA.
R-HSA-168271. Transport of Ribonucleoproteins into the Host Nucleus.
R-HSA-168276. NS1 Mediated Effects on Host Pathways.
R-HSA-168325. Viral Messenger RNA Synthesis.
R-HSA-168333. NEP/NS2 Interacts with the Cellular Export Machinery.
R-HSA-170822. Regulation of Glucokinase by Glucokinase Regulatory Protein.
R-HSA-180746. Nuclear import of Rev protein.
R-HSA-180910. Vpr-mediated nuclear import of PICs.
R-HSA-191859. snRNP Assembly.
R-HSA-3108214. SUMOylation of DNA damage response and repair proteins.
R-HSA-3301854. Nuclear Pore Complex (NPC) Disassembly.
R-HSA-3371453. Regulation of HSF1-mediated heat shock response.
R-HSA-4570464. SUMOylation of RNA binding proteins.
R-HSA-4615885. SUMOylation of DNA replication proteins.
R-HSA-5578749. Transcriptional regulation by small RNAs.
R-HSA-6784531. tRNA processing in the nucleus.

Miscellaneous databases

GeneWikiiTMEM48.
GenomeRNAii55706.
PROiQ9BTX1.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000058804.
CleanExiHS_TMEM48.
GenevisibleiQ9BTX1. HS.

Family and domain databases

InterProiIPR019049. Nucleoporin_prot_Ndc1/Nup.
[Graphical view]
PfamiPF09531. Ndc1_Nup. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiNDC1_HUMAN
AccessioniPrimary (citable) accession number: Q9BTX1
Secondary accession number(s): B4DHA3
, B4DQQ5, G3XA81, Q8NB76, Q9H9T6, Q9NSG3, Q9NSG4, Q9NVZ7
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 16, 2006
Last sequence update: May 16, 2006
Last modified: November 30, 2016
This is version 122 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Miscellaneous

Depletion of NDC1 from HeLa cells interferes with the assembly of phenylalanine-glycine (FG) repeat Nups into nuclear pore complexes.

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Human chromosome 1
    Human chromosome 1: entries, gene names and cross-references to MIM
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.