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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN CD40 LIGAND
 
Authors :  M. Karpusas, Y. M. Hsu, D. Thomas
Date :  05 Jun 97  (Deposition) - 17 Sep 97  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (3x)
Keywords :  Cd40L, Cd40 Ligand, Cytokine, Tnf, Hyper-Igm Syndrome (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Karpusas, Y. M. Hsu, J. H. Wang, J. Thompson, S. Lederman, L. Chess, D. Thomas
2 A Crystal Structure Of An Extracellular Fragment Of Human Cd40 Ligand.
Structure V. 3 1031 1995
PubMed-ID: 8589998  |  Reference-DOI: 10.1016/S0969-2126(01)00239-8
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CD40 LIGAND
    CellT-LYMPHOCYTE
    Cellular LocationMEMBRANE
    Cell LinePICHIA PASTORIS
    ChainsA
    EngineeredYES
    Expression SystemPICHIA PASTORIS
    Expression System Taxid4922
    FragmentEXTRACELLULAR DOMAIN FRAGMENT
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    TissueBLOOD

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (3x)A

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1ALY)

(-) Sites  (0, 0)

(no "Site" information available for 1ALY)

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1A:178 -A:218

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Gly A:116 -Asp A:117
2Asn A:157 -Gly A:158
3Gly A:158 -Lys A:159
4Gln A:186 -Ala A:187
5Ser A:214 -Ala A:215
6Gly A:250 -Thr A:251

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (31, 31)

Asymmetric Unit (31, 31)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
01UniProtVAR_017929G116RCD40L_HUMANDisease (HIGM1)  ---AG116R
02UniProtVAR_017930G116SCD40L_HUMANDisease (HIGM1)  ---AG116S
03UniProtVAR_007514A123ECD40L_HUMANDisease (HIGM1)104894778AA123E
04UniProtVAR_017926H125RCD40L_HUMANDisease (HIGM1)  ---AH125R
05UniProtVAR_007515V126ACD40L_HUMANDisease (HIGM1)  ---AV126A
06UniProtVAR_017931V126DCD40L_HUMANDisease (HIGM1)  ---AV126D
07UniProtVAR_007517W140CCD40L_HUMANDisease (HIGM1)  ---AW140C
08UniProtVAR_007518W140GCD40L_HUMANDisease (HIGM1)104894777AW140G
09UniProtVAR_007519W140RCD40L_HUMANDisease (HIGM1)  ---AW140R
10UniProtVAR_017932K143TCD40L_HUMANDisease (HIGM1)  ---AK143T
11UniProtVAR_007520G144ECD40L_HUMANDisease (HIGM1)  ---AG144E
12UniProtVAR_017922T147NCD40L_HUMANDisease (HIGM1)  ---AT147N
13UniProtVAR_007521L155PCD40L_HUMANDisease (HIGM1)104894769AL155P
14UniProtVAR_017923Y170CCD40L_HUMANDisease (HIGM1)756468554AY170C
15UniProtVAR_017933A173DCD40L_HUMANDisease (HIGM1)  ---AA173D
16UniProtVAR_017927Q174RCD40L_HUMANDisease (HIGM1)  ---AQ174R
17UniProtVAR_017934T176ICD40L_HUMANDisease (HIGM1)  ---AT176I
18UniProtVAR_017935L195PCD40L_HUMANDisease (HIGM1)  ---AL195P
19UniProtVAR_017936A208DCD40L_HUMANDisease (HIGM1)  ---AA208D
20UniProtVAR_007522T211NCD40L_HUMANDisease (HIGM1)  ---AT211N
21UniProtVAR_007523G219RCD40L_HUMANPolymorphism148594123AG219R
22UniProtVAR_017937H224YCD40L_HUMANDisease (HIGM1)  ---AH224Y
23UniProtVAR_017938G226ACD40L_HUMANDisease (HIGM1)  ---AG226A
24UniProtVAR_007524G227VCD40L_HUMANDisease (HIGM1)104894768AG227V
25UniProtVAR_007526L231SCD40L_HUMANDisease (HIGM1)  ---AL231S
26UniProtVAR_007527A235PCD40L_HUMANDisease (HIGM1)104894771AA235P
27UniProtVAR_017939V237ECD40L_HUMANDisease (HIGM1)  ---AV237E
28UniProtVAR_007528T254MCD40L_HUMANDisease (HIGM1)193922136AT254M
29UniProtVAR_017940G257DCD40L_HUMANDisease (HIGM1)  ---AG257D
30UniProtVAR_017928G257SCD40L_HUMANDisease (HIGM1)  ---AG257S
31UniProtVAR_017924L258SCD40L_HUMANDisease (HIGM1)  ---AL258S

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (31, 93)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
01UniProtVAR_017929G116RCD40L_HUMANDisease (HIGM1)  ---AG116R
02UniProtVAR_017930G116SCD40L_HUMANDisease (HIGM1)  ---AG116S
03UniProtVAR_007514A123ECD40L_HUMANDisease (HIGM1)104894778AA123E
04UniProtVAR_017926H125RCD40L_HUMANDisease (HIGM1)  ---AH125R
05UniProtVAR_007515V126ACD40L_HUMANDisease (HIGM1)  ---AV126A
06UniProtVAR_017931V126DCD40L_HUMANDisease (HIGM1)  ---AV126D
07UniProtVAR_007517W140CCD40L_HUMANDisease (HIGM1)  ---AW140C
08UniProtVAR_007518W140GCD40L_HUMANDisease (HIGM1)104894777AW140G
09UniProtVAR_007519W140RCD40L_HUMANDisease (HIGM1)  ---AW140R
10UniProtVAR_017932K143TCD40L_HUMANDisease (HIGM1)  ---AK143T
11UniProtVAR_007520G144ECD40L_HUMANDisease (HIGM1)  ---AG144E
12UniProtVAR_017922T147NCD40L_HUMANDisease (HIGM1)  ---AT147N
13UniProtVAR_007521L155PCD40L_HUMANDisease (HIGM1)104894769AL155P
14UniProtVAR_017923Y170CCD40L_HUMANDisease (HIGM1)756468554AY170C
15UniProtVAR_017933A173DCD40L_HUMANDisease (HIGM1)  ---AA173D
16UniProtVAR_017927Q174RCD40L_HUMANDisease (HIGM1)  ---AQ174R
17UniProtVAR_017934T176ICD40L_HUMANDisease (HIGM1)  ---AT176I
18UniProtVAR_017935L195PCD40L_HUMANDisease (HIGM1)  ---AL195P
19UniProtVAR_017936A208DCD40L_HUMANDisease (HIGM1)  ---AA208D
20UniProtVAR_007522T211NCD40L_HUMANDisease (HIGM1)  ---AT211N
21UniProtVAR_007523G219RCD40L_HUMANPolymorphism148594123AG219R
22UniProtVAR_017937H224YCD40L_HUMANDisease (HIGM1)  ---AH224Y
23UniProtVAR_017938G226ACD40L_HUMANDisease (HIGM1)  ---AG226A
24UniProtVAR_007524G227VCD40L_HUMANDisease (HIGM1)104894768AG227V
25UniProtVAR_007526L231SCD40L_HUMANDisease (HIGM1)  ---AL231S
26UniProtVAR_007527A235PCD40L_HUMANDisease (HIGM1)104894771AA235P
27UniProtVAR_017939V237ECD40L_HUMANDisease (HIGM1)  ---AV237E
28UniProtVAR_007528T254MCD40L_HUMANDisease (HIGM1)193922136AT254M
29UniProtVAR_017940G257DCD40L_HUMANDisease (HIGM1)  ---AG257D
30UniProtVAR_017928G257SCD40L_HUMANDisease (HIGM1)  ---AG257S
31UniProtVAR_017924L258SCD40L_HUMANDisease (HIGM1)  ---AL258S

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

(-) PROSITE Motifs  (2, 2)

Asymmetric Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TNF_2PS50049 TNF family profile.CD40L_HUMAN123-261  1A:123-261
2TNF_1PS00251 TNF family signature.CD40L_HUMAN161-177  1A:161-177
Biological Unit 1 (2, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TNF_2PS50049 TNF family profile.CD40L_HUMAN123-261  3A:123-261
2TNF_1PS00251 TNF family signature.CD40L_HUMAN161-177  3A:161-177

(-) Exons   (3, 3)

Asymmetric Unit (3, 3)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003706291aENSE00001453187X:135730352-135730563212CD40L_HUMAN1-52520--
1.2ENST000003706292ENSE00000677016X:135732425-135732556132CD40L_HUMAN53-96440--
1.3ENST000003706293ENSE00000677017X:135736532-13573658958CD40L_HUMAN97-116201A:116-1161
1.4ENST000003706294ENSE00000677018X:135738515-13573857763CD40L_HUMAN116-137221A:116-13722
1.5ENST000003706295ENSE00001125156X:135741198-1357425491352CD40L_HUMAN137-2611251A:137-261125

(-) 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:146
 aligned with CD40L_HUMAN | P29965 from UniProtKB/Swiss-Prot  Length:261

    Alignment length:146
                                   125       135       145       155       165       175       185       195       205       215       225       235       245       255      
          CD40L_HUMAN   116 GDQNPQIAAHVISEASSKTTSVLQWAEKGYYTMSNNLVTLENGKQLTVKRQGLYYIYAQVTFCSNREASSQAPFIASLCLKSPGRFERILLRAANTHSSAKPCGQQSIHLGGVFELQPGASVFVNVTDPSQVSHGTGFTSFGLLKL 261
               SCOP domains d1alya_ A: Extracellular domain of CD40 ligand                                                                                                     SCOP domains
               CATH domains 1alyA00 A:116-261  [code=2.60.120.40, no name defined]                                                                                             CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeee.........................eeee...eeee...eeeeeeeeeeeee........eeeeeeeee......eeeeeeeee.......eeeeeeeeeeeee....eeeeee..hhh........eeeeee. Sec.struct. author
             SAPs(SNPs) (1) R------E-RA-------------C--TE--N-------P--------------C--DR-I------------------P------------D--N-------R----Y-AV---S---P-E----------------M--DS--- SAPs(SNPs) (1)
             SAPs(SNPs) (2) S---------D-------------G--------------------------------------------------------------------------------------------------------------------S---- SAPs(SNPs) (2)
             SAPs(SNPs) (3) ------------------------R------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (3)
                PROSITE (1) -------TNF_2  PDB: A:123-261 UniProt: 123-261                                                                                                      PROSITE (1)
                PROSITE (2) ---------------------------------------------TNF_1            ------------------------------------------------------------------------------------ PROSITE (2)
           Transcript 1 (1) 1--------------------Exon 1.5  PDB: A:137-261 UniProt: 137-261                                                                                     Transcript 1 (1)
           Transcript 1 (2) Exon 1.4              ---------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 1aly A 116 GDQNPQIAAHVISEASSKTTSVLQWAEKGYYTMSNNLVTLENGKQLTVKRQGLYYIYAQVTFCSNREASSQAPFIASLCLKSPGRFERILLRAANTHSSAKPCGQQSIHLGGVFELQPGASVFVNVTDPSQVSHGTGFTSFGLLKL 261
                                   125       135       145       155       165       175       185       195       205       215       225       235       245       255      

   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  (1, 1)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (33, 33)

Asymmetric Unit(hide GO term definitions)
Chain A   (CD40L_HUMAN | P29965)
molecular function
    GO:0005174    CD40 receptor binding    Interacting selectively and non-covalently with CD40, a receptor found on the surface of all B-lymphocytes.
    GO:0005125    cytokine activity    Functions to control the survival, growth, differentiation and effector function of tissues and cells.
    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:0005164    tumor necrosis factor receptor binding    Interacting selectively and non-covalently with the tumor necrosis factor receptor.
biological process
    GO:0030183    B cell differentiation    The process in which a precursor cell type acquires the specialized features of a B cell. A B cell is a lymphocyte of B lineage with the phenotype CD19-positive and capable of B cell mediated immunity.
    GO:0042100    B cell proliferation    The expansion of a B cell population by cell division. Follows B cell activation.
    GO:0031295    T cell costimulation    The process of providing, via surface-bound receptor-ligand pairs, a second, antigen-independent, signal in addition to that provided by the T cell receptor to augment T cell activation.
    GO:0007257    activation of JUN kinase activity    The initiation of the activity of the inactive enzyme JUN kinase (JNK).
    GO:0006955    immune response    Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat.
    GO:0048305    immunoglobulin secretion    The regulated release of immunoglobulins from a B cell or plasma cell, whose mechanism includes the use of alternate polyadenylylation signals to favor the biosynthesis of secreted forms of immunoglobulin over membrane-bound immunoglobulin.
    GO:0006954    inflammatory response    The immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents. The process is characterized by local vasodilation, extravasation of plasma into intercellular spaces and accumulation of white blood cells and macrophages.
    GO:0045190    isotype switching    The switching of activated B cells from IgM biosynthesis to biosynthesis of other isotypes of immunoglobulin, accomplished through a recombination process involving an intrachromosomal deletion involving switch regions that reside 5' of each constant region gene segment in the immunoglobulin heavy chain locus.
    GO:0007159    leukocyte cell-cell adhesion    The attachment of a leukocyte to another cell via adhesion molecules.
    GO:0043066    negative regulation of apoptotic process    Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process.
    GO:0030168    platelet activation    A series of progressive, overlapping events triggered by exposure of the platelets to subendothelial tissue. These events include shape change, adhesiveness, aggregation, and release reactions. When carried through to completion, these events lead to the formation of a stable hemostatic plug.
    GO:0051092    positive regulation of NF-kappaB transcription factor activity    Any process that activates or increases the frequency, rate or extent of activity of the transcription factor NF-kappaB.
    GO:0042102    positive regulation of T cell proliferation    Any process that activates or increases the rate or extent of T cell proliferation.
    GO:2000353    positive regulation of endothelial cell apoptotic process    Any process that activates or increases the frequency, rate or extent of endothelial cell apoptotic process.
    GO:0032733    positive regulation of interleukin-10 production    Any process that activates or increases the frequency, rate, or extent of interleukin-10 production.
    GO:0032735    positive regulation of interleukin-12 production    Any process that activates or increases the frequency, rate, or extent of interleukin-12 production.
    GO:0032753    positive regulation of interleukin-4 production    Any process that activates or increases the frequency, rate, or extent of interleukin-4 production.
    GO:0050776    regulation of immune response    Any process that modulates the frequency, rate or extent of the immune response, the immunological reaction of an organism to an immunogenic stimulus.
    GO:0051023    regulation of immunoglobulin secretion    Any process that modulates the frequency, rate or extent of the regulated release of immunoglobulins from a cell.
    GO:0033209    tumor necrosis factor-mediated signaling pathway    A series of molecular signals initiated by the binding of a tumor necrosis factor to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription.
cellular component
    GO:0009986    cell surface    The external part of the cell wall and/or plasma membrane.
    GO:0009897    external side of plasma membrane    The leaflet of the plasma membrane that faces away from the cytoplasm and any proteins embedded or anchored in it or attached to its surface.
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0005887    integral component of plasma membrane    The component of the plasma membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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 Related Entries

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

UniProtKB/Swiss-Prot
        CD40L_HUMAN | P299651i9r 3lkj 3qd6

(-) Related Entries Specified in the PDB File

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