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Protein

Lamin-B2

Gene

LMNB2

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

Functioni

Lamins are components of the nuclear lamina, a fibrous layer on the nucleoplasmic side of the inner nuclear membrane, which is thought to provide a framework for the nuclear envelope and may also interact with chromatin.

GO - Molecular functioni

Complete GO annotation...

Enzyme and pathway databases

BioCyciZFISH:ENSG00000099858-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Lamin-B2
Gene namesi
Name:LMNB2
Synonyms:LMN2
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 19

Organism-specific databases

HGNCiHGNC:6638. LMNB2.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Intermediate filament, Membrane, Nucleus

Pathology & Biotechi

Involvement in diseasei

Partial acquired lipodystrophy (APLD)2 Publications
The disease is caused by mutations affecting the gene represented in this entry.
Disease descriptionA rare childhood disease characterized by loss of subcutaneous fat from the face and trunk. Fat deposition on the pelvic girdle and lower limbs is normal or excessive. Most frequently, onset between 5 and 15 years of age. Most affected subjects are females and some show no other abnormality, but many develop glomerulonephritis, diabetes mellitus, hyperlipidemia, and complement deficiency. Mental retardation in some cases. APLD is a sporadic disorder of unknown etiology.
See also OMIM:608709
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_031063235R → Q in APLD. 1 PublicationCorresponds to variant rs61726481dbSNPEnsembl.1
Natural variantiVAR_074171252Y → H in APLD. 1 Publication1
Natural variantiVAR_031064427A → T in APLD. 1 PublicationCorresponds to variant rs57521499dbSNPEnsembl.1
Epilepsy, progressive myoclonic 9 (EPM9)1 Publication
The disease may be caused by mutations affecting the gene represented in this entry.
Disease descriptionAn autosomal recessive form of progressive myoclonic epilepsy, a rare disease initially responsive to antiepileptic drugs which over time becomes refractory and can be associated with cognitive decline. EPM9 features include myoclonus, tonic-clonic seizures, ataxia, and psychomotor development.
See also OMIM:616540
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_074170157H → Y in EPM9; disrupts fibrillar formation. 1 Publication1

Keywords - Diseasei

Disease mutation, Epilepsy

Organism-specific databases

DisGeNETi84823.
MalaCardsiLMNB2.
MIMi608709. phenotype.
616540. phenotype.
OpenTargetsiENSG00000176619.
Orphaneti79087. Partial acquired lipodystrophy.
PharmGKBiPA30404.

Polymorphism and mutation databases

BioMutaiLMNB2.
DMDMi23503078.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000638201 – 617Lamin-B2Add BLAST617
PropeptideiPRO_0000403470618 – 620Removed in mature formBy similarity3

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei23PhosphothreonineCombined sources1
Modified residuei34PhosphothreonineCombined sources1
Modified residuei37PhosphoserineCombined sources1
Cross-linki77Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources
Modified residuei81N6-acetyllysine; alternateCombined sources1
Cross-linki81Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2); alternateCombined sources
Cross-linki195Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources
Modified residuei316PhosphoserineCombined sources1
Modified residuei420PhosphoserineCombined sources1
Modified residuei422PhosphoserineCombined sources1
Modified residuei424PhosphoserineCombined sources1
Modified residuei426PhosphoserineCombined sources1
Modified residuei433Omega-N-methylarginineBy similarity1
Modified residuei497PhosphoserineCombined sources1
Modified residuei617Cysteine methyl esterBy similarity1
Lipidationi617S-farnesyl cysteineBy similarity1

Post-translational modificationi

B-type lamins undergo a series of modifications, such as farnesylation and phosphorylation. Increased phosphorylation of the lamins occurs before envelope disintegration and probably plays a role in regulating lamin associations.

Keywords - PTMi

Acetylation, Isopeptide bond, Lipoprotein, Methylation, Phosphoprotein, Prenylation, Ubl conjugation

Proteomic databases

EPDiQ03252.
MaxQBiQ03252.
PaxDbiQ03252.
PeptideAtlasiQ03252.
PRIDEiQ03252.

2D gel databases

REPRODUCTION-2DPAGEIPI00009771.

PTM databases

iPTMnetiQ03252.
PhosphoSitePlusiQ03252.
SwissPalmiQ03252.

Expressioni

Gene expression databases

BgeeiENSG00000176619.
CleanExiHS_LMNB2.
ExpressionAtlasiQ03252. baseline and differential.

Organism-specific databases

HPAiCAB022593.
HPA047863.
HPA062477.

Interactioni

Subunit structurei

Interacts with TMEM43.By similarity

Binary interactionsi

WithEntry#Exp.IntActNotes
PIBF1A0A087WUI64EBI-2830427,EBI-11749468

Protein-protein interaction databases

BioGridi124281. 34 interactors.
DIPiDIP-57724N.
IntActiQ03252. 36 interactors.
MINTiMINT-3024955.
STRINGi9606.ENSP00000462730.

Structurei

Secondary structure

1620
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi473 – 479Combined sources7
Beta strandi484 – 490Combined sources7
Beta strandi492 – 494Combined sources3
Beta strandi502 – 507Combined sources6
Beta strandi512 – 516Combined sources5
Beta strandi528 – 533Combined sources6
Helixi534 – 536Combined sources3
Turni542 – 544Combined sources3
Beta strandi545 – 548Combined sources4
Beta strandi552 – 555Combined sources4
Beta strandi558 – 565Combined sources8
Beta strandi571 – 580Combined sources10

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2LLLNMR-A469-589[»]
5BNWX-ray2.40D403-415[»]
ProteinModelPortaliQ03252.
SMRiQ03252.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini465 – 578LTDAdd BLAST114

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni1 – 48HeadAdd BLAST48
Regioni49 – 400RodAdd BLAST352
Regioni49 – 83Coil 1AAdd BLAST35
Regioni84 – 95Linker 1Add BLAST12
Regioni96 – 229Coil 1BAdd BLAST134
Regioni230 – 256Linker 2Add BLAST27
Regioni257 – 400Coil 2Add BLAST144
Regioni401 – 620TailAdd BLAST220

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi435 – 440Nuclear localization signalSequence analysis6

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi590 – 602Asp/Glu-rich (highly acidic; could be involved in chromatin binding)Add BLAST13

Sequence similaritiesi

Belongs to the intermediate filament family.Curated
Contains 1 LTD domain.Curated

Keywords - Domaini

Coiled coil

Phylogenomic databases

eggNOGiKOG0977. Eukaryota.
ENOG410Y2H6. LUCA.
GeneTreeiENSGT00830000128282.
HOGENOMiHOG000007711.
HOVERGENiHBG013015.
InParanoidiQ03252.
KOiK07611.
OMAiFRKNVFE.
TreeFamiTF101181.

Family and domain databases

Gene3Di2.60.40.1260. 1 hit.
InterProiIPR001664. IF.
IPR018039. Intermediate_filament_CS.
IPR027696. Lamin_B.
IPR001322. Lamin_tail_dom.
[Graphical view]
PANTHERiPTHR23239. PTHR23239. 1 hit.
PTHR23239:SF152. PTHR23239:SF152. 1 hit.
PfamiPF00038. Filament. 1 hit.
PF00932. LTD. 1 hit.
[Graphical view]
SMARTiSM01391. Filament. 1 hit.
[Graphical view]
SUPFAMiSSF74853. SSF74853. 1 hit.
PROSITEiPS00226. IF. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

Q03252-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSPPSPGRRR EQRRPRAAAT MATPLPGRAG GPATPLSPTR LSRLQEKEEL
60 70 80 90 100
RELNDRLAHY IDRVRALELE NDRLLLKISE KEEVTTREVS GIKALYESEL
110 120 130 140 150
ADARRVLDET ARERARLQIE IGKLRAELDE VNKSAKKREG ELTVAQGRVK
160 170 180 190 200
DLESLFHRSE VELAAALSDK RGLESDVAEL RAQLAKAEDG HAVAKKQLEK
210 220 230 240 250
ETLMRVDLEN RCQSLQEELD FRKSVFEEEV RETRRRHERR LVEVDSSRQQ
260 270 280 290 300
EYDFKMAQAL EELRSQHDEQ VRLYKLELEQ TYQAKLDSAK LSSDQNDKAA
310 320 330 340 350
SAAREELKEA RMRLESLSYQ LSGLQKQASA AEDRIRELEE AMAGERDKFR
360 370 380 390 400
KMLDAKEQEM TEMRDVMQQQ LAEYQELLDV KLALDMEINA YRKLLEGEEE
410 420 430 440 450
RLKLSPSPSS RVTVSRATSS SSGSLSATGR LGRSKRKRLE VEEPLGSGPS
460 470 480 490 500
VLGTGTGGSG GFHLAQQASA SGSVSIEEID LEGKFVQLKN NSDKDQSLGN
510 520 530 540 550
WRIKRQVLEG EEIAYKFTPK YILRAGQMVT VWAAGAGVAH SPPSTLVWKG
560 570 580 590 600
QSSWGTGESF RTVLVNADGE EVAMRTVKKS SVMRENENGE EEEEEAEFGE
610 620
EDLFHQQGDP RTTSRGCYVM
Length:620
Mass (Da):69,948
Last modified:November 11, 2015 - v4
Checksum:iA8799BB12B6242B9
GO

Sequence cautioni

The sequence AAH06551 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti401R → S in AAA80979 (PubMed:1630457).Curated1
Sequence conflicti439 – 475LEVEE…SGSVS → WRWRSPWQRPKRPGHGHGWQ RWLPPGPAGLGLGQRH in AAA80979 (PubMed:1630457).CuratedAdd BLAST37

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_074170157H → Y in EPM9; disrupts fibrillar formation. 1 Publication1
Natural variantiVAR_031063235R → Q in APLD. 1 PublicationCorresponds to variant rs61726481dbSNPEnsembl.1
Natural variantiVAR_036370236R → W in a colorectal cancer sample; somatic mutation. 1 PublicationCorresponds to variant rs774297966dbSNPEnsembl.1
Natural variantiVAR_074171252Y → H in APLD. 1 Publication1
Natural variantiVAR_031064427A → T in APLD. 1 PublicationCorresponds to variant rs57521499dbSNPEnsembl.1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BT007441 mRNA. Translation: AAP36109.1.
AC011522 Genomic DNA. No translation available.
AC005624 Genomic DNA. Translation: AAC34573.1.
BC006551 mRNA. Translation: AAH06551.1. Different initiation.
M94362 mRNA. Translation: AAA80979.1.
M94363 Genomic DNA. Translation: AAB00873.1. Sequence problems.
CCDSiCCDS12090.2.
RefSeqiNP_116126.3. NM_032737.3.
UniGeneiHs.538286.

Genome annotation databases

EnsembliENST00000325327; ENSP00000327054; ENSG00000176619.
GeneIDi84823.
KEGGihsa:84823.

Keywords - Coding sequence diversityi

Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BT007441 mRNA. Translation: AAP36109.1.
AC011522 Genomic DNA. No translation available.
AC005624 Genomic DNA. Translation: AAC34573.1.
BC006551 mRNA. Translation: AAH06551.1. Different initiation.
M94362 mRNA. Translation: AAA80979.1.
M94363 Genomic DNA. Translation: AAB00873.1. Sequence problems.
CCDSiCCDS12090.2.
RefSeqiNP_116126.3. NM_032737.3.
UniGeneiHs.538286.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2LLLNMR-A469-589[»]
5BNWX-ray2.40D403-415[»]
ProteinModelPortaliQ03252.
SMRiQ03252.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi124281. 34 interactors.
DIPiDIP-57724N.
IntActiQ03252. 36 interactors.
MINTiMINT-3024955.
STRINGi9606.ENSP00000462730.

PTM databases

iPTMnetiQ03252.
PhosphoSitePlusiQ03252.
SwissPalmiQ03252.

Polymorphism and mutation databases

BioMutaiLMNB2.
DMDMi23503078.

2D gel databases

REPRODUCTION-2DPAGEIPI00009771.

Proteomic databases

EPDiQ03252.
MaxQBiQ03252.
PaxDbiQ03252.
PeptideAtlasiQ03252.
PRIDEiQ03252.

Protocols and materials databases

DNASUi84823.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000325327; ENSP00000327054; ENSG00000176619.
GeneIDi84823.
KEGGihsa:84823.

Organism-specific databases

CTDi84823.
DisGeNETi84823.
GeneCardsiLMNB2.
HGNCiHGNC:6638. LMNB2.
HPAiCAB022593.
HPA047863.
HPA062477.
MalaCardsiLMNB2.
MIMi150341. gene.
608709. phenotype.
616540. phenotype.
neXtProtiNX_Q03252.
OpenTargetsiENSG00000176619.
Orphaneti79087. Partial acquired lipodystrophy.
PharmGKBiPA30404.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG0977. Eukaryota.
ENOG410Y2H6. LUCA.
GeneTreeiENSGT00830000128282.
HOGENOMiHOG000007711.
HOVERGENiHBG013015.
InParanoidiQ03252.
KOiK07611.
OMAiFRKNVFE.
TreeFamiTF101181.

Enzyme and pathway databases

BioCyciZFISH:ENSG00000099858-MONOMER.

Miscellaneous databases

ChiTaRSiLMNB2. human.
GenomeRNAii84823.
PROiQ03252.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000176619.
CleanExiHS_LMNB2.
ExpressionAtlasiQ03252. baseline and differential.

Family and domain databases

Gene3Di2.60.40.1260. 1 hit.
InterProiIPR001664. IF.
IPR018039. Intermediate_filament_CS.
IPR027696. Lamin_B.
IPR001322. Lamin_tail_dom.
[Graphical view]
PANTHERiPTHR23239. PTHR23239. 1 hit.
PTHR23239:SF152. PTHR23239:SF152. 1 hit.
PfamiPF00038. Filament. 1 hit.
PF00932. LTD. 1 hit.
[Graphical view]
SMARTiSM01391. Filament. 1 hit.
[Graphical view]
SUPFAMiSSF74853. SSF74853. 1 hit.
PROSITEiPS00226. IF. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiLMNB2_HUMAN
AccessioniPrimary (citable) accession number: Q03252
Secondary accession number(s): O75292, Q14734, Q96DF6
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 1, 1994
Last sequence update: November 11, 2015
Last modified: November 30, 2016
This is version 173 of the entry and version 4 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

The structural integrity of the lamina is strictly controlled by the cell cycle, as seen by the disintegration and formation of the nuclear envelope in prophase and telophase, respectively.

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. Human chromosome 19
    Human chromosome 19: 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. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  6. 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.