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(-) Description

Title :  COMPLEX OF HIGH-AFFINITY SIRP ALPHA VARIANT FD6 WITH CD47
 
Authors :  A. M. Ring, E. Ozkan, C. C. M. Ho, K. C. Garcia
Date :  04 May 13  (Deposition) - 12 Jun 13  (Release) - 28 Aug 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.93
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Immunoglobulin Fold, Immune Regulation, N-Linked Glycosylation, Plasma Membrane, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  K. Weiskopf, A. M. Ring, C. C. Ho, J. P. Volkmer, A. M. Levin, A. K. Volkmer, E. Ozkan, N. B. Fernhoff, M. Van De Rijn, I. L. Weissman K. C. Garcia
Engineered Sirp Alpha Variants As Immunotherapeutic Adjuvants To Anticancer Antibodies.
Science V. 341 88 2013
PubMed-ID: 23722425  |  Reference-DOI: 10.1126/SCIENCE.1238856

(-) Compounds

Molecule 1 - LEUKOCYTE SURFACE ANTIGEN CD47
    ChainsA, C
    EngineeredYES
    Expression SystemTRICHOPLUSIA NI
    Expression System PlasmidPACGP67A
    Expression System Taxid7111
    Expression System Vector TypePLASMID
    GeneCD47, MER6
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymANTIGENIC SURFACE DETERMINANT PROTEIN OA3, INTEGRIN- ASSOCIATED PROTEIN, IAP, PROTEIN MER6
 
Molecule 2 - HIGH-AFFINITY SIRPA VARIANT FD6
    ChainsB, D
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPMAL-P2X
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)AB  
Biological Unit 2 (1x)  CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 13)

Asymmetric Unit (3, 13)
No.NameCountTypeFull Name
1NAG8Ligand/IonN-ACETYL-D-GLUCOSAMINE
2PCA2Mod. Amino AcidPYROGLUTAMIC ACID
3SO43Ligand/IonSULFATE ION
Biological Unit 1 (3, 5)
No.NameCountTypeFull Name
1NAG3Ligand/IonN-ACETYL-D-GLUCOSAMINE
2PCA1Mod. Amino AcidPYROGLUTAMIC ACID
3SO41Ligand/IonSULFATE ION
Biological Unit 2 (3, 8)
No.NameCountTypeFull Name
1NAG5Ligand/IonN-ACETYL-D-GLUCOSAMINE
2PCA1Mod. Amino AcidPYROGLUTAMIC ACID
3SO42Ligand/IonSULFATE ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELYS A:6 , THR A:107 , ILE A:108 , HOH A:333 , HOH A:334BINDING SITE FOR RESIDUE SO4 A 201
02AC2SOFTWAREASN A:32 , HOH A:318 , HOH A:323 , HOH A:326 , HOH A:331 , HOH A:335 , HOH A:342 , HOH A:344 , HOH A:354 , SO4 D:201BINDING SITE FOR RESIDUE NAG A 202
03AC3SOFTWAREASN A:55 , LYS C:43BINDING SITE FOR RESIDUE NAG A 203
04AC4SOFTWAREASN A:93 , GLU A:110BINDING SITE FOR RESIDUE NAG A 204
05AC5SOFTWAREASN C:32BINDING SITE FOR RESIDUE NAG C 201
06AC6SOFTWAREASN C:5 , THR C:7 , PHE C:24 , VAL D:13 , SER D:20 , ILE D:22BINDING SITE FOR RESIDUE NAG C 202
07AC7SOFTWAREGLU C:11 , PHE C:12 , ASN C:16 , VAL C:19 , VAL C:20BINDING SITE FOR RESIDUE NAG C 203
08AC8SOFTWARELYS A:43 , ARG C:45 , ASN C:55 , PRO C:60 , THR C:61 , ASP C:62 , HOH C:343BINDING SITE FOR RESIDUE NAG C 204
09AC9SOFTWAREGLY C:92 , ASN C:93 , GLU C:110BINDING SITE FOR RESIDUE NAG C 205
10BC1SOFTWARELYS C:6 , THR C:107 , ILE C:108 , HOH C:333 , HOH C:370 , HOH C:371BINDING SITE FOR RESIDUE SO4 C 206
11BC2SOFTWARENAG A:202 , LYS C:41 , ARG D:53 , GLN D:54 , HOH D:392BINDING SITE FOR RESIDUE SO4 D 201

(-) SS Bonds  (4, 4)

Asymmetric Unit
No.Residues
1A:23 -A:96
2B:25 -B:91
3C:23 -C:96
4D:25 -D:91

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Phe B:31 -Pro B:32
2Gly B:55 -Pro B:56
3Ser B:98 -Pro B:99
4Phe D:31 -Pro D:32
5Gly D:55 -Pro D:56
6Ser D:98 -Pro D:99

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4KJY)

(-) 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:114
                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........eee......eeee..........hhh.eeeeeee..eeeeeee....eee........ee.hhhhhhh...eeeehhhhhh...eeeeeeee..eeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------ Transcript
                 4kjy A   1 xLLFNKTKSVEFTFGNDTVVIPCFVTNMEAQNTTEVYVKWKFKGRDIYTFDGALNKSTVPTDFSSAKIEVSQLLKGDASLKMDKSDAVSHTGNYTCEVTELTREGETIIELKYR 114
                            |       10        20        30        40        50        60        70        80        90       100       110    
                            |                                                                                                                 
                            1-PCA                                                                                                             

Chain B from PDB  Type:PROTEIN  Length:114
                                                                                                                                                  
               SCOP domains d4kjyb_ B: automated matches                                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....ee....eeee.....eee..ee........eeeee......eeee.........eee.............eee...hhhhheeeeeeeee.....eeeee...eeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------ Transcript
                 4kjy B   1 EEEVQIIQPDKSVSVAAGESAILHCTITSLFPVGPIQWFRGAGPARVLIYNQRQGPFPRVTTISETTRRENMDFSISISNITPADAGTYYCIKFRKGSPDTEFKSGAGTELSVR 114
                                    10        20        30        40        50        60        70        80        90       100       110    

Chain C from PDB  Type:PROTEIN  Length:114
                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...ee...eee......eeee..ee......hhh.eeeeeee..eeeeeee....eee.hhhhh....hhhhhhhh...eeeehhhhhh..eeeeeeeee..eeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------ Transcript
                 4kjy C   1 xLLFNKTKSVEFTFGNDTVVIPCFVTNMEAQNTTEVYVKWKFKGRDIYTFDGALNKSTVPTDFSSAKIEVSQLLKGDASLKMDKSDAVSHTGNYTCEVTELTREGETIIELKYR 114
                            |       10        20        30        40        50        60        70        80        90       100       110    
                            1-PCA                                                                                                             

Chain D from PDB  Type:PROTEIN  Length:116
                                                                                                                                                    
               SCOP domains d4kjyd_ D: automated matches                                                                                         SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee....eeeee....eee..ee........eeeee......eeee.........eee.............eee...hhhhheeeeeeeee.....eeeee...eeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------- Transcript
                 4kjy D   2 EEVQIIQPDKSVSVAAGESAILHCTITSLFPVGPIQWFRGAGPARVLIYNQRQGPFPRVTTISETTRRENMDFSISISNITPADAGTYYCIKFRKGSPDTEFKSGAGTELSVRAKP 117
                                    11        21        31        41        51        61        71        81        91       101       111      

   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, 2)

Asymmetric Unit

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (18, 18)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

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        CD47_HUMAN | Q087222jjs 2jjt 2vsc 4cmm 5iwl 5tz2 5tzt 5tzu

(-) Related Entries Specified in the PDB File

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