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(-) Description

Title :  CRYSTAL STRUCTURE OF LAMIN-B1
 
Authors :  C. Xu, C. B. Bian, M. F. Amaya, C. Bountra, J. Weigelt, C. H. Arrowsmith, A. M. Edwards, A. Bochkarev, J. Min, Structural Genomics Consortiu
Date :  14 Nov 11  (Deposition) - 30 Nov 11  (Release) - 07 Mar 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Keywords :  Structural Genomics Consortium, Sgc, Ig-Like Domain, Intermediate Filament, Lipoprotein, Membrane, Nucleus, Structural Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. Ruan, C. Xu, C. Bian, R. Lam, J. P. Wang, J. Kania, J. Min, J. Zang
Crystal Structures Of The Coil 2B Fragment And The Globular Tail Domain Of Human Lamin B1.
Febs Lett. V. 586 314 2012
PubMed-ID: 22265972  |  Reference-DOI: 10.1016/J.FEBSLET.2012.01.007

(-) Compounds

Molecule 1 - LAMIN-B1
    ChainsA, B, C
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentGLOBULAR TAIL DOMAIN, UNP RESIDUES 428-550
    GeneLMNB1, LMN2, LMNB
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit ABC
Biological Unit 1 (1x)A  
Biological Unit 2 (1x) B 
Biological Unit 3 (1x)  C

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 3UMN)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Pro A:509 -Pro A:510
2Pro B:509 -Pro B:510
3Pro C:509 -Pro C:510

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 6)

Asymmetric Unit (2, 6)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_071077A436VLMNB1_HUMANUnclassified  ---A/B/CA436V
2UniProtVAR_031646A501VLMNB1_HUMANPolymorphism36105360A/B/CA501V

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_071077A436VLMNB1_HUMANUnclassified  ---AA436V
2UniProtVAR_031646A501VLMNB1_HUMANPolymorphism36105360AA501V

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_071077A436VLMNB1_HUMANUnclassified  ---BA436V
2UniProtVAR_031646A501VLMNB1_HUMANPolymorphism36105360BA501V

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 3 (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_071077A436VLMNB1_HUMANUnclassified  ---CA436V
2UniProtVAR_031646A501VLMNB1_HUMANPolymorphism36105360CA501V

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3UMN)

(-) Exons   (0, 0)

(no "Exon" information available for 3UMN)

(-) 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:118
 aligned with LMNB1_HUMAN | P20700 from UniProtKB/Swiss-Prot  Length:586

    Alignment length:118
                                   440       450       460       470       480       490       500       510       520       530       540        
          LMNB1_HUMAN   431 SISHSASATGNVCIEEIDVDGKFIRLKNTSEQDQPMGGWEMIRKIGDTSVSYKYTSRYVLKAGQTVTIWAANAGVTASPPTDLIWKNQNSWGTGEDVKVILKNSQGEEVAQRSTVFKT 548
               SCOP domains d3umna_ A: automated matches                                                                                           SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee...eeeeee.....eeeeee.....ee....eeeeee..eeeeee.....ee....eeeeee...........eeee...........eeeeee.....eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -----V----------------------------------------------------------------V----------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                 3umn A 431 SISHSASATGNVCIEEIDVDGKFIRLKNTSEQDQPMGGWEMIRKIGDTSVSYKYTSRYVLKAGQTVTIWAANAGVTASPPTDLIWKNQNSWGTGEDVKVILKNSQGEEVAQRSTVFKT 548
                                   440       450       460       470       480       490       500       510       520       530       540        

Chain B from PDB  Type:PROTEIN  Length:116
 aligned with LMNB1_HUMAN | P20700 from UniProtKB/Swiss-Prot  Length:586

    Alignment length:116
                                   441       451       461       471       481       491       501       511       521       531       541      
          LMNB1_HUMAN   432 ISHSASATGNVCIEEIDVDGKFIRLKNTSEQDQPMGGWEMIRKIGDTSVSYKYTSRYVLKAGQTVTIWAANAGVTASPPTDLIWKNQNSWGTGEDVKVILKNSQGEEVAQRSTVFK 547
               SCOP domains d3umnb_ B: automated matches                                                                                         SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee...eeeeee.....eeeeee.....ee....eeeeee..eeeeee.....ee....eeeeee...........eeee...........eeeeee.....eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----V----------------------------------------------------------------V---------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------- Transcript
                 3umn B 432 ISHSASATGNVCIEEIDVDGKFIRLKNTSEQDQPMGGWEMIRKIGDTSVSYKYTSRYVLKAGQTVTIWAANAGVTASPPTDLIWKNQNSWGTGEDVKVILKNSQGEEVAQRSTVFK 547
                                   441       451       461       471       481       491       501       511       521       531       541      

Chain C from PDB  Type:PROTEIN  Length:118
 aligned with LMNB1_HUMAN | P20700 from UniProtKB/Swiss-Prot  Length:586

    Alignment length:118
                                   440       450       460       470       480       490       500       510       520       530       540        
          LMNB1_HUMAN   431 SISHSASATGNVCIEEIDVDGKFIRLKNTSEQDQPMGGWEMIRKIGDTSVSYKYTSRYVLKAGQTVTIWAANAGVTASPPTDLIWKNQNSWGTGEDVKVILKNSQGEEVAQRSTVFKT 548
               SCOP domains d3umnc_ C: automated matches                                                                                           SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee...eeeeee.....eeeeee.....ee....eeeeee..eeeeee.....ee....eeeee............eee............eeeeee.....eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -----V----------------------------------------------------------------V----------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                 3umn C 431 SISHSASATGNVCIEEIDVDGKFIRLKNTSEQDQPMGGWEMIRKIGDTSVSYKYTSRYVLKAGQTVTIWAANAGVTASPPTDLIWKNQNSWGTGEDVKVILKNSQGEEVAQRSTVFKT 548
                                   440       450       460       470       480       490       500       510       520       530       540        

   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, 3)

Asymmetric Unit

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (LMNB1_HUMAN | P20700)
molecular function
    GO:0043274    phospholipase binding    Interacting selectively and non-covalently with any phospholipase, enzymes that catalyze of the hydrolysis of a glycerophospholipid.
    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.
cellular component
    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:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    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:0005637    nuclear inner membrane    The inner, i.e. lumen-facing, lipid bilayer of the nuclear envelope.
    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: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.

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    Pro A:509 - Pro A:510   [ RasMol ]  
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        LMNB1_HUMAN | P207002kpw 3jt0 3tyy

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