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Protein

Lamin-B2

Gene

LMNB2

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: -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.

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.

GO - Molecular functioni

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

EuPathDBiHostDB:ENSG00000176619.10
HGNCiHGNC:6638 LMNB2
MIMi150341 gene
neXtProtiNX_Q03252

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

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_074171252Y → H in APLD. 1 Publication1
Natural variantiVAR_031064427A → T in APLD. 1 PublicationCorresponds to variant dbSNP:rs57521499EnsemblClinVar.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 PublicationCorresponds to variant dbSNP:rs797045143EnsemblClinVar.1

Keywords - Diseasei

Disease mutation, Epilepsy

Organism-specific databases

DisGeNETi84823
MalaCardsiLMNB2
MIMi608709 phenotype
616540 phenotype
OpenTargetsiENSG00000176619
Orphaneti79087 Acquired partial lipodystrophy
457265 Progressive myoclonic epilepsy type 9
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
Cross-linki255Glycyl 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
Cross-linki489Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources
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
ProteomicsDBi58204

2D gel databases

REPRODUCTION-2DPAGEiIPI00009771

PTM databases

iPTMnetiQ03252
PhosphoSitePlusiQ03252
SwissPalmiQ03252

Expressioni

Gene expression databases

BgeeiENSG00000176619 Expressed in 148 organ(s), highest expression level in testis
CleanExiHS_LMNB2

Organism-specific databases

HPAiCAB022593
HPA047863
HPA062477

Interactioni

Subunit structurei

Interacts with TMEM43.By similarity

Binary interactionsi

Protein-protein interaction databases

BioGridi124281, 49 interactors
DIPiDIP-57724N
IntActiQ03252, 45 interactors
MINTiQ03252
STRINGi9606.ENSP00000462730

Structurei

Secondary structure

1620
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

ProteinModelPortaliQ03252
SMRiQ03252
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini46 – 402IF rodPROSITE-ProRule annotationAdd BLAST357
Domaini462 – 579LTDPROSITE-ProRule annotationAdd BLAST118

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni1 – 48HeadAdd BLAST48
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.PROSITE-ProRule annotation

Keywords - Domaini

Coiled coil

Phylogenomic databases

eggNOGiKOG0977 Eukaryota
ENOG410Y2H6 LUCA
GeneTreeiENSGT00910000143989
HOGENOMiHOG000007711
HOVERGENiHBG013015
InParanoidiQ03252
KOiK07611
OMAiEEIAYKF
TreeFamiTF101181

Family and domain databases

Gene3Di2.60.40.1260, 1 hit
InterProiView protein in InterPro
IPR001664 IF
IPR018039 IF_conserved
IPR039008 IF_rod_dom
IPR001322 Lamin_tail_dom
IPR036415 Lamin_tail_dom_sf
PANTHERiPTHR23239 PTHR23239, 1 hit
PfamiView protein in Pfam
PF00038 Filament, 1 hit
PF00932 LTD, 1 hit
SMARTiView protein in SMART
SM01391 Filament, 1 hit
SUPFAMiSSF74853 SSF74853, 1 hit
PROSITEiView protein in PROSITE
PS00226 IF_ROD_1, 1 hit
PS51842 IF_ROD_2, 1 hit
PS51841 LTD, 1 hit

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 PublicationCorresponds to variant dbSNP:rs797045143EnsemblClinVar.1
Natural variantiVAR_031063235R → Q Polymorphism; may be a risk factor for partial aquired lipodystrophy. 2 PublicationsCorresponds to variant dbSNP:rs121912497EnsemblClinVar.1
Natural variantiVAR_036370236R → W in a colorectal cancer sample; somatic mutation. 1 PublicationCorresponds to variant dbSNP:rs774297966Ensembl.1
Natural variantiVAR_074171252Y → H in APLD. 1 Publication1
Natural variantiVAR_031064427A → T in APLD. 1 PublicationCorresponds to variant dbSNP:rs57521499EnsemblClinVar.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

Similar proteinsi

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, 49 interactors
DIPiDIP-57724N
IntActiQ03252, 45 interactors
MINTiQ03252
STRINGi9606.ENSP00000462730

PTM databases

iPTMnetiQ03252
PhosphoSitePlusiQ03252
SwissPalmiQ03252

Polymorphism and mutation databases

BioMutaiLMNB2
DMDMi23503078

2D gel databases

REPRODUCTION-2DPAGEiIPI00009771

Proteomic databases

EPDiQ03252
MaxQBiQ03252
PaxDbiQ03252
PeptideAtlasiQ03252
PRIDEiQ03252
ProteomicsDBi58204

Protocols and materials databases

DNASUi84823
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000325327; ENSP00000327054; ENSG00000176619
GeneIDi84823
KEGGihsa:84823

Organism-specific databases

CTDi84823
DisGeNETi84823
EuPathDBiHostDB:ENSG00000176619.10
GeneCardsiLMNB2
HGNCiHGNC:6638 LMNB2
HPAiCAB022593
HPA047863
HPA062477
MalaCardsiLMNB2
MIMi150341 gene
608709 phenotype
616540 phenotype
neXtProtiNX_Q03252
OpenTargetsiENSG00000176619
Orphaneti79087 Acquired partial lipodystrophy
457265 Progressive myoclonic epilepsy type 9
PharmGKBiPA30404
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG0977 Eukaryota
ENOG410Y2H6 LUCA
GeneTreeiENSGT00910000143989
HOGENOMiHOG000007711
HOVERGENiHBG013015
InParanoidiQ03252
KOiK07611
OMAiEEIAYKF
TreeFamiTF101181

Miscellaneous databases

ChiTaRSiLMNB2 human
GenomeRNAii84823
PROiPR:Q03252
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000176619 Expressed in 148 organ(s), highest expression level in testis
CleanExiHS_LMNB2

Family and domain databases

Gene3Di2.60.40.1260, 1 hit
InterProiView protein in InterPro
IPR001664 IF
IPR018039 IF_conserved
IPR039008 IF_rod_dom
IPR001322 Lamin_tail_dom
IPR036415 Lamin_tail_dom_sf
PANTHERiPTHR23239 PTHR23239, 1 hit
PfamiView protein in Pfam
PF00038 Filament, 1 hit
PF00932 LTD, 1 hit
SMARTiView protein in SMART
SM01391 Filament, 1 hit
SUPFAMiSSF74853 SSF74853, 1 hit
PROSITEiView protein in PROSITE
PS00226 IF_ROD_1, 1 hit
PS51842 IF_ROD_2, 1 hit
PS51841 LTD, 1 hit
ProtoNetiSearch...

Entry informationi

Entry nameiLMNB2_HUMAN
AccessioniPrimary (citable) accession number: Q03252
Secondary accession number(s): O75292, Q14734, Q96DF6
Entry historyiIntegrated into UniProtKB/Swiss-Prot: June 1, 1994
Last sequence update: November 11, 2015
Last modified: November 7, 2018
This is version 191 of the entry and version 4 of the sequence. See 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

Keywords - Technical termi

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

Documents

  1. SIMILARITY comments
    Index of protein domains and families
  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. Human chromosome 19
    Human chromosome 19: entries, gene names and cross-references to MIM
  6. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
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Main funding by: National Institutes of Health

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