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(-) Description

Title :  CRYSTAL STRUCTURE OF KKOFAB IN COMPLEX WITH PLATELET FACTOR 4
 
Authors :  Z. Cai, Z. Zhu, Q. Liu, M. I. Greene
Date :  08 Sep 14  (Deposition) - 16 Dec 15  (Release) - 27 Jan 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  4.11
Chains :  Asym. Unit :  A,B,C,D,H,L,M,N
Biol. Unit 1:  B,D,H,L  (1x)
Biol. Unit 2:  A,C,M,N  (1x)
Keywords :  Kko, Pf4, Hit, Immunoglobulin, Cxc Chemokine, Antibody, Antigen, Blood, Immune System-Cytokine Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Z. Cai, S. V. Yarovoi, Z. Zhu, L. Rauova, V. Hayes, T. Lebedeva, Q. Liu, M. Poncz, G. Arepally, D. B. Cines, M. I. Greene
Atomic Description Of The Immune Complex Involved In Heparin-Induced Thrombocytopenia.
Nat Commun V. 6 8277 2015
PubMed-ID: 26391892  |  Reference-DOI: 10.1038/NCOMMS9277

(-) Compounds

Molecule 1 - PLATELET FACTOR 4
    Chains: D, C, B, A
    Engineered: YES
    Expression System: DROSOPHILA MELANOGASTER
    Expression System Cell Line: S2 CELLS
    Expression System Taxid: 7227
    Gene: PF4, CXCL4, SCYB4
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: PF-4, C-X-C MOTIF CHEMOKINE 4, IROPLACT, ONCOSTATIN-A, PLATELET FACTOR 4, SHORT FORM
 
Molecule 2 - PLATELET FACTOR 4 ANTIBODY KKO LIGHT CHAIN
    Chains: L, M
    Engineered: YES
    Expression System: MUS MUSCULUS
    Expression System Cell Line: HYBRIDOMA
    Expression System Taxid: 10090
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
 
Molecule 3 - PLATELET FACTOR 4 ANTIBODY KKO HEAVY CHAIN
    Chains: H, N
    Engineered: YES
    Expression System: MUS MUSCULUS
    Expression System Cell Line: HYBRIDOMA
    Expression System Taxid: 10090
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ABCDHLMN
Biological Unit 1 (1x):  B DHL  
Biological Unit 2 (1x): A C   MN

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 4R9Y)

(-) Sites  (0, 0)

(no "Site" information available for 4R9Y)

(-) SS Bonds  (18, 18)

Asymmetric Unit
No.Residues
1A:10 -A:36
2A:12 -A:52
3B:10 -B:36
4B:12 -B:52
5C:10 -C:36
6C:12 -C:52
7D:10 -D:36
8D:12 -D:52
9H:21 -H:95
10H:146 -H:201
11L:48 -L:113
12L:159 -L:219
13L:239 -H:134
14M:48 -M:113
15M:159 -M:219
16M:239 -N:134
17N:21 -N:95
18N:146 -N:201

(-) Cis Peptide Bonds  (8, 8)

Asymmetric Unit
No.Residues
1Tyr L:119 -Pro L:120
2Tyr L:165 -Pro L:166
3Arg H:39 -Pro H:40
4Phe H:152 -Pro H:153
5Tyr M:119 -Pro M:120
6Tyr M:165 -Pro M:166
7Arg N:39 -Pro N:40
8Phe N:152 -Pro N:153

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4R9Y)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4R9Y)

(-) Exons   (0, 0)

(no "Exon" information available for 4R9Y)

(-) 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:65
                                                                                                 
               SCOP domains ----------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------- Pfam domains
         Sec.struct. author ..................eeeeeee.........eeeeee....eee.....hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------- Transcript
                 4r9y A   6 GDLQCLCVKTTSQVRPRHITSLEVIKAGPHCPTAQLIATLKNGRKICLDLQAPLYKKIIKKLLES  70
                                    15        25        35        45        55        65     


Chain B from PDB  Type:PROTEIN  Length:65
                                                                                                 
               SCOP domains ----------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------- Pfam domains
         Sec.struct. author ..................eeeeeee.........eeeeee....eee.....hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------- Transcript
                 4r9y B   6 GDLQCLCVKTTSQVRPRHITSLEVIKAGPHCPTAQLIATLKNGRKICLDLQAPLYKKIIKKLLES  70
                                    15        25        35        45        55        65     


Chain C from PDB  Type:PROTEIN  Length:65
                                                                                                 
               SCOP domains ----------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------- Pfam domains
         Sec.struct. author ....................eeeee.........eeeee.....ee.......hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------- Transcript
                 4r9y C   6 GDLQCLCVKTTSQVRPRHITSLEVIKAGPHCPTAQLIATLKNGRKICLDLQAPLYKKIIKKLLES  70
                                    15        25        35        45        55        65     


Chain D from PDB  Type:PROTEIN  Length:65
                                                                                                 
               SCOP domains ----------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------- Pfam domains
         Sec.struct. author ....................eeeee.........eeeee.....ee.......hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------- Transcript
                 4r9y D   6 GDLQCLCVKTTSQVRPRHITSLEVIKAGPHCPTAQLIATLKNGRKICLDLQAPLYKKIIKKLLES  70
                                    15        25        35        45        55        65     


Chain H from PDB  Type:PROTEIN  Length:218
                                                                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eee.....................eeeeee.....eeeeeee.................eeeee....eeeee.........eeeeee................eeeee........eeeee.............eeeeeeee.....eeee...........eeeeee..eeeeeeee...........eeeeee......eeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4r9y H   1 VQLQQSGAELVKPGASVKLSCKASGYTFTNYFIYWVKQRPGQGLEWIGEINPRNGDTDFNEKFESRATLTVDKSSSTAYMQLSSLTSEDSAIYYCTRSPYGNNYGFTYWGQGTLVTVSAAKTTPPSVYPLAPGCGDAAGSSVTLGCLVKGYFPESVTVTWNSGSLSSSVHTFPALLQSGLYTMSSSVTVPSSTWPSQTVTCSVAHPASSTTVDKKLEP 218
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210        


Chain L from PDB  Type:PROTEIN  Length:214
                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee.............eeeeeee.......eeeeee.....eeeeee...ee.......eeee....eeeeee...hhhhh.eeeeee...........ee..........eeeee..hhhhhh......eeeeeee.....eeeeee........eeeee.........eeeeeee...hhhhhhh..eeeeee................. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4r9y L  26 DIQMIQSQKFMSTSVGDRVTVTCKASQNVGTNVAWYQQKPGQSPNALIYSASYRYSGVPDRFTGSGSGTDFTLTITNVQSEDLADYFCQQYNSYPLTFGTGTKLDLKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC 239
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235    


Chain M from PDB  Type:PROTEIN  Length:214
                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee.............eeeeeee.......eeeeee.....eeeeee...ee.......eeee....eeeeee...hhhhh.eeeeee...........ee..........eeeee..............eeeeeee.....eeeeee.........eeee.........eeeeee....hhhhhhh.eeeeeee..........eee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4r9y M  26 DIQMIQSQKFMSTSVGDRVTVTCKASQNVGTNVAWYQQKPGQSPNALIYSASYRYSGVPDRFTGSGSGTDFTLTITNVQSEDLADYFCQQYNSYPLTFGTGTKLDLKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC 239
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235    


Chain N from PDB  Type:PROTEIN  Length:218
                                                                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eee.....................eeeeee.....eeeeeee......eee........eeeee....eeeee.........eeeeee................eeeee........eeeee.............eeeeeeee.....eeee........eeeeeeeee..eeeeeeee...........eeeeeee....eee..ee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4r9y N   1 VQLQQSGAELVKPGASVKLSCKASGYTFTNYFIYWVKQRPGQGLEWIGEINPRNGDTDFNEKFESRATLTVDKSSSTAYMQLSSLTSEDSAIYYCTRSPYGNNYGFTYWGQGTLVTVSAAKTTPPSVYPLAPGCGDAAGSSVTLGCLVKGYFPESVTVTWNSGSLSSSVHTFPALLQSGLYTMSSSVTVPSSTWPSQTVTCSVAHPASSTTVDKKLEP 218
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210
   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  (0, 0)

(no "SCOP Domain" information available for 4R9Y)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4R9Y)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4R9Y)

(-) Gene Ontology  (31, 31)

Asymmetric Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Arg H:39 - Pro H:40   [ RasMol ]  
    Arg N:39 - Pro N:40   [ RasMol ]  
    Phe H:152 - Pro H:153   [ RasMol ]  
    Phe N:152 - Pro N:153   [ RasMol ]  
    Tyr L:119 - Pro L:120   [ RasMol ]  
    Tyr L:165 - Pro L:166   [ RasMol ]  
    Tyr M:119 - Pro M:120   [ RasMol ]  
    Tyr M:165 - Pro M:166   [ RasMol ]  
 
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 Related Entries

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

UniProtKB/Swiss-Prot
        PLF4_HUMAN | P02776: 1dn3 1f9q 1f9r 1f9s 1pfm 1pfn 1rhp 4r9w 4rau

(-) Related Entries Specified in the PDB File

4r97 KKOFAB ONLY
4r9w PLATELET FACTOR 4