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(-) Description

Title :  STRUCTURE OF COIL 2B OF HUMAN LAMIN
 
Authors :  M. Bollati, M Bolognesi
Date :  16 Dec 11  (Deposition) - 22 Feb 12  (Release) - 22 Feb 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (2x)
Keywords :  Structural Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Bollati, A. Barbiroli, V. Favalli, E. Arbustini, P. Charron, M. Bolognesi
Structures Of The Lamin A/C R335W And E347K Mutants: Implications For Dilated Cardiolaminopathies.
Biochem. Biophys. Res. Commun. V. 418 217 2012
PubMed-ID: 22266370  |  Reference-DOI: 10.1016/J.BBRC.2011.12.136

(-) Compounds

Molecule 1 - PRELAMIN-A/C
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    GeneLMNA, LMN1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymLAMIN-A/C, 70 KDA LAMIN, RENAL CARCINOMA ANTIGEN NY-REN-32

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (1x)A
Biological Unit 2 (2x)A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3V5B)

(-) Sites  (0, 0)

(no "Site" information available for 3V5B)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3V5B)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3V5B)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (12, 12)

Asymmetric Unit (12, 12)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
01UniProtVAR_039775E317KLMNA_HUMANDisease (CMD1A)56816490AE317K
02UniProtVAR_070179A318TLMNA_HUMANDisease (CMD1A)267607574AA318T
03UniProtVAR_009983R336QLMNA_HUMANDisease (EDMD2)58105277AR336Q
04UniProtVAR_009984R343QLMNA_HUMANDisease (EDMD2)61177390AR343Q
05UniProtVAR_039776R349LLMNA_HUMANDisease (CMD1A)58789393AR349L
06UniProtVAR_009985E358KLMNA_HUMANDisease (MDCL)60458016AE358K
07UniProtVAR_064970E361KLMNA_HUMANDisease (EDMD2)267607634AE361K
08UniProtVAR_009986M371KLMNA_HUMANDisease (EDMD2)59653062AM371K
09UniProtVAR_016205R377HLMNA_HUMANDisease (LGMD1B)61672878AR377H
10UniProtVAR_039777R377LLMNA_HUMANDisease (LGMD1B)61672878AR377L
11UniProtVAR_063591L380SLMNA_HUMANDisease (MDCL)121912495AL380S
12UniProtVAR_009987R386KLMNA_HUMANDisease (EDMD2)267607545AR386K

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (12, 12)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
01UniProtVAR_039775E317KLMNA_HUMANDisease (CMD1A)56816490AE317K
02UniProtVAR_070179A318TLMNA_HUMANDisease (CMD1A)267607574AA318T
03UniProtVAR_009983R336QLMNA_HUMANDisease (EDMD2)58105277AR336Q
04UniProtVAR_009984R343QLMNA_HUMANDisease (EDMD2)61177390AR343Q
05UniProtVAR_039776R349LLMNA_HUMANDisease (CMD1A)58789393AR349L
06UniProtVAR_009985E358KLMNA_HUMANDisease (MDCL)60458016AE358K
07UniProtVAR_064970E361KLMNA_HUMANDisease (EDMD2)267607634AE361K
08UniProtVAR_009986M371KLMNA_HUMANDisease (EDMD2)59653062AM371K
09UniProtVAR_016205R377HLMNA_HUMANDisease (LGMD1B)61672878AR377H
10UniProtVAR_039777R377LLMNA_HUMANDisease (LGMD1B)61672878AR377L
11UniProtVAR_063591L380SLMNA_HUMANDisease (MDCL)121912495AL380S
12UniProtVAR_009987R386KLMNA_HUMANDisease (EDMD2)267607545AR386K

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (12, 24)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
01UniProtVAR_039775E317KLMNA_HUMANDisease (CMD1A)56816490AE317K
02UniProtVAR_070179A318TLMNA_HUMANDisease (CMD1A)267607574AA318T
03UniProtVAR_009983R336QLMNA_HUMANDisease (EDMD2)58105277AR336Q
04UniProtVAR_009984R343QLMNA_HUMANDisease (EDMD2)61177390AR343Q
05UniProtVAR_039776R349LLMNA_HUMANDisease (CMD1A)58789393AR349L
06UniProtVAR_009985E358KLMNA_HUMANDisease (MDCL)60458016AE358K
07UniProtVAR_064970E361KLMNA_HUMANDisease (EDMD2)267607634AE361K
08UniProtVAR_009986M371KLMNA_HUMANDisease (EDMD2)59653062AM371K
09UniProtVAR_016205R377HLMNA_HUMANDisease (LGMD1B)61672878AR377H
10UniProtVAR_039777R377LLMNA_HUMANDisease (LGMD1B)61672878AR377L
11UniProtVAR_063591L380SLMNA_HUMANDisease (MDCL)121912495AL380S
12UniProtVAR_009987R386KLMNA_HUMANDisease (EDMD2)267607545AR386K

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1IFPS00226 Intermediate filaments signature.LMNA_HUMAN373-381  1A:373-381
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1IFPS00226 Intermediate filaments signature.LMNA_HUMAN373-381  1A:373-381
Biological Unit 2 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1IFPS00226 Intermediate filaments signature.LMNA_HUMAN373-381  2A:373-381

(-) Exons   (2, 2)

Asymmetric Unit (2, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.9cENST000003683009cENSE00001169671chr1:156084498-156085065568LMNA_HUMAN1-1191190--
1.15aENST0000036830015aENSE00001169588chr1:156100408-156100564157LMNA_HUMAN119-171530--
1.16dENST0000036830016dENSE00001054499chr1:156104194-156104319126LMNA_HUMAN172-213420--
1.17bENST0000036830017bENSE00001054502chr1:156104596-156104766171LMNA_HUMAN214-270570--
1.18cENST0000036830018cENSE00001054494chr1:156104978-156105103126LMNA_HUMAN271-312420--
1.19cENST0000036830019cENSE00001054501chr1:156105692-156105912221LMNA_HUMAN313-386741A:313-38674
1.20cENST0000036830020cENSE00001054498chr1:156106005-156106227223LMNA_HUMAN386-460751A:386-3861
1.20fENST0000036830020fENSE00001245117chr1:156106712-156106819108LMNA_HUMAN461-496360--
1.20hENST0000036830020hENSE00001054491chr1:156106904-156107023120LMNA_HUMAN497-536400--
1.21bENST0000036830021bENSE00001244973chr1:156107445-15610753490LMNA_HUMAN537-566300--
1.21iENST0000036830021iENSE00001054507chr1:156108279-156108548270LMNA_HUMAN567-656900--
1.22gENST0000036830022gENSE00001834579chr1:156108871-1561098801010LMNA_HUMAN657-66480--

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:74
 aligned with LMNA_HUMAN | P02545 from UniProtKB/Swiss-Prot  Length:664

    Alignment length:74
                                   322       332       342       352       362       372       382    
           LMNA_HUMAN   313 LAAKEAKLRDLEDSLARERDTSRRLLAEKEREMAEMRARMQQQLDEYQELLDIKLALDMEIHAYRKLLEGEEER 386
               SCOP domains d3v5ba_ A: automated matches                                               SCOP domains
               CATH domains -------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
             SAPs(SNPs) (1) ----KT-----------------Q------Q-----L--------K--K---------K-----H--S-----K SAPs(SNPs) (1)
             SAPs(SNPs) (2) ----------------------------------------------------------------L--------- SAPs(SNPs) (2)
                    PROSITE ------------------------------------------------------------IF       ----- PROSITE
           Transcript 1 (1) Exon 1.19c  PDB: A:313-386 UniProt: 313-386                                Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------------------------------1 Transcript 1 (2)
                 3v5b A 313 LAAKEAKLRDLEDSLARERDTSRRLLAEKEREMAEMRARMQQQLDEYQELLDIKLALDMEIHAYRKLLEGEEER 386
                                   322       332       342       352       362       372       382    

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3V5B)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3V5B)

(-) Gene Ontology  (35, 35)

Asymmetric Unit(hide GO term definitions)
Chain A   (LMNA_HUMAN | P02545)
molecular function
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0008157    protein phosphatase 1 binding    Interacting selectively and non-covalently with the enzyme protein phosphatase 1.
    GO:0005198    structural molecule activity    The action of a molecule that contributes to the structural integrity of a complex or its assembly within or outside a cell.
biological process
    GO:0036498    IRE1-mediated unfolded protein response    A series of molecular signals mediated by the endoplasmic reticulum stress sensor IRE1 (Inositol-requiring transmembrane kinase/endonuclease). Begins with activation of IRE1 in response to endoplasmic reticulum (ER) stress, and ends with regulation of a downstream cellular process, e.g. transcription. One target of activated IRE1 is the transcription factor HAC1 in yeast, or XBP1 in mammals; IRE1 cleaves an intron of a mRNA coding for HAC1/XBP1 to generate an activated HAC1/XBP1 transcription factor, which controls the up regulation of UPR-related genes. At least in mammals, IRE1 can also signal through additional intracellular pathways including JNK and NF-kappaB.
    GO:0071456    cellular response to hypoxia    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating lowered oxygen tension. Hypoxia, defined as a decline in O2 levels below normoxic levels of 20.8 - 20.95%, results in metabolic adaptation at both the cellular and organismal level.
    GO:0030951    establishment or maintenance of microtubule cytoskeleton polarity    Any cellular process that results in the specification, formation or maintenance of polarized microtubule-based cytoskeletal structures.
    GO:0007077    mitotic nuclear envelope disassembly    The cell cycle process in which the controlled breakdown of the nuclear envelope during mitotic cell division occurs.
    GO:0007084    mitotic nuclear envelope reassembly    The cell cycle process that results in reformation of the nuclear envelope during mitotic cell division.
    GO:0007517    muscle organ development    The process whose specific outcome is the progression of the muscle over time, from its formation to the mature structure. The muscle is an organ consisting of a tissue made up of various elongated cells that are specialized to contract and thus to produce movement and mechanical work.
    GO:1904178    negative regulation of adipose tissue development    Any process that stops, prevents or reduces the frequency, rate or extent of adipose tissue development.
    GO:2001237    negative regulation of extrinsic apoptotic signaling pathway    Any process that stops, prevents or reduces the frequency, rate or extent of extrinsic apoptotic signaling pathway.
    GO:0090201    negative regulation of release of cytochrome c from mitochondria    Any process that decreases the rate, frequency or extent of release of cytochrome c from mitochondria, the process in which cytochrome c is enabled to move from the mitochondrial intermembrane space into the cytosol, which is an early step in apoptosis and leads to caspase activation.
    GO:0006998    nuclear envelope organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the nuclear envelope.
    GO:0006997    nucleus organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the nucleus.
    GO:0090343    positive regulation of cell aging    Any process that increases the rate, frequency, or extent of cell aging. Cell aging is the progression of the cell from its inception to the end of its lifespan.
    GO:0045669    positive regulation of osteoblast differentiation    Any process that activates or increases the frequency, rate or extent of osteoblast differentiation.
    GO:0034504    protein localization to nucleus    A process in which a protein transports or maintains the localization of another protein to the nucleus.
    GO:0030334    regulation of cell migration    Any process that modulates the frequency, rate or extent of cell migration.
    GO:1900180    regulation of protein localization to nucleus    Any process that modulates the frequency, rate or extent of protein localization to nucleus.
    GO:0009612    response to mechanical stimulus    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a mechanical stimulus.
    GO:0007283    spermatogenesis    The process of formation of spermatozoa, including spermatocytogenesis and spermiogenesis.
    GO:0035105    sterol regulatory element binding protein import into nucleus    The transfer of a sterol regulatory element binding protein (SREBP) into the nucleus, across the nuclear membrane, in response to altered levels of one or more lipids. SREBPs are transcription factors that bind sterol regulatory elements (SREs), DNA motifs found in the promoters of target genes.
    GO:0055015    ventricular cardiac muscle cell development    The process whose specific outcome is the progression of a ventricular cardiac muscle cell over time, from its formation to the mature state. Cardiac muscle cells are striated muscle cells that are responsible for heart contraction. The ventricle is the part of the heart that pumps blood out of the organ.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0005882    intermediate filament    A cytoskeletal structure that forms a distinct elongated structure, characteristically 10 nm in diameter, that occurs in the cytoplasm of eukaryotic cells. Intermediate filaments form a fibrous system, composed of chemically heterogeneous subunits and involved in mechanically integrating the various components of the cytoplasmic space. Intermediate filaments may be divided into five chemically distinct classes: Type I, acidic keratins; Type II, basic keratins; Type III, including desmin, vimentin and others; Type IV, neurofilaments and related filaments; and Type V, lamins.
    GO:0005638    lamin filament    Any of a group of intermediate-filament proteins that form the fibrous matrix on the inner surface of the nuclear envelope. They are classified as lamins A, B and C.
    GO:0005635    nuclear envelope    The double lipid bilayer enclosing the nucleus and separating its contents from the rest of the cytoplasm; includes the intermembrane space, a gap of width 20-40 nm (also called the perinuclear space).
    GO:0005652    nuclear lamina    The fibrous, electron-dense layer lying on the nucleoplasmic side of the inner membrane of a cell nucleus, composed of lamin filaments. The polypeptides of the lamina are thought to be concerned in the dissolution of the nuclear envelope and its re-formation during mitosis. The lamina is composed of lamin A and lamin C filaments cross-linked into an orthogonal lattice, which is attached via lamin B to the inner nuclear membrane through interactions with a lamin B receptor, an IFAP, in the membrane.
    GO:0016363    nuclear matrix    The dense fibrillar network lying on the inner side of the nuclear membrane.
    GO:0031965    nuclear membrane    Either of the lipid bilayers that surround the nucleus and form the nuclear envelope; excludes the intermembrane space.
    GO:0016607    nuclear speck    A discrete extra-nucleolar subnuclear domain, 20-50 in number, in which splicing factors are seen to be localized by immunofluorescence microscopy.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
    GO:0048471    perinuclear region of cytoplasm    Cytoplasm situated near, or occurring around, the nucleus.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        LMNA_HUMAN | P025451ifr 1ivt 1x8y 2xv5 2ypt 3gef 3v4q 3v4w

(-) Related Entries Specified in the PDB File

3v4q STRUCTURE OF R335W MUTANT OF HUMAN LAMIN
3v4w STRUCTURE OF E347K MUTANT OF LAMIN