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(-) Description

Title :  STRUCTURE OF LAMIN A/C GLOBULAR DOMAIN
 
Authors :  S. Dhe-Paganon, E. D. Werner, S. E. Shoelson
Date :  13 Apr 01  (Deposition) - 17 Jul 02  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.40
Chains :  Asym./Biol. Unit :  A
Keywords :  Immunoglobulin, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Dhe-Paganon, E. D. Werner, Y. I. Chi, S. E. Shoelson
Structure Of The Globular Tail Of Nuclear Lamin.
J. Biol. Chem. V. 277 17381 2002
PubMed-ID: 11901143  |  Reference-DOI: 10.1074/JBC.C200038200

(-) Compounds

Molecule 1 - LAMIN A/C
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentRESIDUES 436-552
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:20 , HOH A:68 , TRP A:498 , GLY A:503 , ALA A:504 , THR A:505 , HIS A:506 , SER A:507 , ASP A:511 , VAL A:513 , LYS A:515BINDING SITE FOR RESIDUE GOL A 600

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1IFR)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Pro A:508 -Pro A:509

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (38, 38)

Asymmetric/Biological Unit (38, 38)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
01UniProtVAR_039779R435CLMNA_HUMANDisease (CMD1A)150840924AR435C
02UniProtVAR_070181R439CLMNA_HUMANDisease (FPLD2)62636506AR439C
03UniProtVAR_039780D446VLMNA_HUMANDisease (EDMD2)58541611AD446V
04UniProtVAR_064971G449DLMNA_HUMANDisease (EDMD2)267607637AG449D
05UniProtVAR_063592R453PLMNA_HUMANDisease (MDCL)267607598AR453P
06UniProtVAR_009988R453WLMNA_HUMANDisease (EDMD2)58932704AR453W
07UniProtVAR_064972L454PLMNA_HUMANDisease (EDMD2)267607638AL454P
08UniProtVAR_063593R455PLMNA_HUMANDisease (MDCL)267607597AR455P
09UniProtVAR_063594N456DLMNA_HUMANDisease (MDCL)267607599AN456D
10UniProtVAR_039781N456ILMNA_HUMANDisease (EDMD2)60992550AN456I
11UniProtVAR_039782N456KLMNA_HUMANDisease (EDMD2)61235244AN456K
12UniProtVAR_064973D461YLMNA_HUMANDisease (EDMD2)267607642AD461Y
13UniProtVAR_009989G465DLMNA_HUMANDisease (FPLD2)61282106AG465D
14UniProtVAR_064974W467RLMNA_HUMANDisease (EDMD2)267607639AW467R
15UniProtVAR_009990I469TLMNA_HUMANDisease (EDMD2)57394692AI469T
16UniProtVAR_017662R471CLMNA_HUMANDisease (HGPS)28928902AR471C
17UniProtVAR_070182R471HLMNA_HUMANDisease (CMD1A)267607578AR471H
18UniProtVAR_039783Y481HLMNA_HUMANDisease (LGMD1B)57747780AY481H
19UniProtVAR_009991R482LLMNA_HUMANDisease (FPLD2)11575937AR482L
20UniProtVAR_009992R482QLMNA_HUMANDisease (FPLD2)11575937AR482Q
21UniProtVAR_009993R482WLMNA_HUMANDisease (FPLD2)57920071AR482W
22UniProtVAR_009994K486NLMNA_HUMANDisease (FPLD2)59981161AK486N
23UniProtVAR_072825T488PLMNA_HUMANPolymorphism267607607AT488P
24UniProtVAR_071968K515ELMNA_HUMANDisease (FPLD2)  ---AK515E
25UniProtVAR_039784W520SLMNA_HUMANDisease (EDMD2)58362413AW520S
26UniProtVAR_067258G523RLMNA_HUMANDisease (CMD1A)201583907AG523R
27UniProtVAR_017663R527CLMNA_HUMANDisease (HGPS)57318642AR527C
28UniProtVAR_018727R527HLMNA_HUMANDisease (MADA)57520892AR527H
29UniProtVAR_009995R527PLMNA_HUMANDisease (FPLD2)57520892AR527P
30UniProtVAR_009996T528KLMNA_HUMANDisease (EDMD2)57629361AT528K
31UniProtVAR_039785T528RLMNA_HUMANDisease (EDMD2)57629361AT528R
32UniProtVAR_034709A529VLMNA_HUMANDisease (MADA)60580541AA529V
33UniProtVAR_009997L530PLMNA_HUMANDisease (EDMD2)60934003AL530P
34UniProtVAR_039786R541CLMNA_HUMANPolymorphism56984562AR541C
35UniProtVAR_039787R541HLMNA_HUMANDisease (EDMD2)61444459AR541H
36UniProtVAR_064975R541PLMNA_HUMANDisease (EDMD2)61444459AR541P
37UniProtVAR_039788R541SLMNA_HUMANDisease (EDMD2)56984562AR541S
38UniProtVAR_034710K542NLMNA_HUMANDisease (HGPS)56673169AK542N

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1IFR)

(-) Exons   (4, 4)

Asymmetric/Biological Unit (4, 4)
 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_HUMAN313-386740--
1.20cENST0000036830020cENSE00001054498chr1:156106005-156106227223LMNA_HUMAN386-460751A:432-460 (gaps)61
1.20fENST0000036830020fENSE00001245117chr1:156106712-156106819108LMNA_HUMAN461-496361A:461-49636
1.20hENST0000036830020hENSE00001054491chr1:156106904-156107023120LMNA_HUMAN497-536401A:497-53640
1.21bENST0000036830021bENSE00001244973chr1:156107445-15610753490LMNA_HUMAN537-566301A:537-5448
1.21iENST0000036830021iENSE00001054507chr1:156108279-156108548270LMNA_HUMAN567-656900--
1.22gENST0000036830022gENSE00001834579chr1:156108871-1561098801010LMNA_HUMAN657-66480--

(-) Sequences/Alignments

Asymmetric/Biological 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:113
 aligned with LMNA_HUMAN | P02545 from UniProtKB/Swiss-Prot  Length:664

    Alignment length:145
                                   409       419       429       439       449       459       469       479       489       499       509       519       529       539     
           LMNA_HUMAN   400 GRASSHSSQTQGGGSVTKKRKLESTESRSSFSQHARTSGRVAVEEVDEEGKFVRLRNKSNEDQSMGNWQIKRQNGDDPLLTYRFPPKFTLKAGQVVTIWAAGAGATHSPPTDLVWKAQNTWGCGNSLRTALINSTGEEVAMRKLV 544
               SCOP domains d   1i                             fra_ A: Lamin A/C globular tail domain                                                                         SCOP domains
               CATH domains 1   if                             rA00 A:432-544  [code=2.60.40.1260, no name defined]                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .---ee-----------------------------ee...eeeeee.....eeeeee.....ee....eeeeee.....eeee.....ee....eeeeee...........eeee...........eeeeee.....eeeeeee. Sec.struct. author
             SAPs(SNPs) (1) -----------------------------------C---C------V--D---PPPD----Y---D-R-T-C---------HL---N-P--------------------------E----S--R---CKVP----------CN-- SAPs(SNPs) (1)
             SAPs(SNPs) (2) -----------------------------------------------------W--I--------------H----------Q--------------------------------------------HR------------H--- SAPs(SNPs) (2)
             SAPs(SNPs) (3) --------------------------------------------------------K-------------------------W--------------------------------------------P-------------P--- SAPs(SNPs) (3)
             SAPs(SNPs) (4) ---------------------------------------------------------------------------------------------------------------------------------------------S--- SAPs(SNPs) (4)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.20c  PDB: A:432-460 (gaps) UniProt: 386-460           Exon 1.20f  PDB: A:461-496          Exon 1.20h  PDB: A:497-536              1.21b    Transcript 1
                 1ifr A 432 G---SH-----------------------------RTSGRVAVEEVDEEGKFVRLRNKSNEDQSMGNWQIKRQNGDDPLLTYRFPPKFTLKAGQVVTIWAAGAGATHSPPTDLVWKAQNTWGCGNSLRTALINSTGEEVAMRKLV 544
                            |   ||   -         -         -     | 439       449       459       469       479       489       499       509       519       529       539     
                            | 433|                           435                                                                                                             
                          432  434                                                                                                                                           

   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/Biological Unit

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1IFR)

(-) Gene Ontology  (35, 35)

Asymmetric/Biological 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 | P025451ivt 1x8y 2xv5 2ypt 3gef 3v4q 3v4w 3v5b

(-) Related Entries Specified in the PDB File

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