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(-) Description

Title :  INTEGRIN I DOMAIN OF COMPLEMENT RECEPTOR 3 IN COMPLEX WITH C3D
 
Authors :  G. Bajic, L. Yatime, T. Vorup-Jensen, G. R. Andersen
Date :  12 Aug 13  (Deposition) - 02 Oct 13  (Release) - 12 Nov 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Integrin, Complement Receptor, Immunity, Innate Immunity, Inflammation, Phagocytosis, Mac-1, Cd11B/Cd18, Alphambeta2, Macrophage, Rossmann Fold, I Domain, Von Willebrand Factor A (Vwa), Alpha-Alpha Barrel, Adhesion, Cell Adhesion (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Bajic, L. Yatime, R. B. Sim, T. Vorup-Jensen, G. R. Andersen
Structural Insight On The Recognition Of Surface-Bound Opsonins By The Integrin I Domain Of Complement Receptor 3.
Proc. Natl. Acad. Sci. Usa V. 110 16426 2013
PubMed-ID: 24065820  |  Reference-DOI: 10.1073/PNAS.1311261110

(-) Compounds

Molecule 1 - COMPLEMENT C3
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PETM-20
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 994-1288
    Gene: C3, CPAMD1
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: C3 AND PZP-LIKE ALPHA-2-MACROGLOBULIN DOMAIN-CONTAINING PROTEIN 1, COMPLEMENT C3 BETA CHAIN, COMPLEMENT C3 ALPHA CHAIN, C3A ANAPHYLATOXIN, ACYLATION STIMULATING PROTEIN, ASP, C3ADESARG, COMPLEMENT C3B ALPHA' CHAIN, COMPLEMENT C3C ALPHA' CHAIN FRAGMENT 1, COMPLEMENT C3DG FRAGMENT, COMPLEMENT C3G FRAGMENT, COMPLEMENT C3D FRAGMENT, COMPLEMENT C3F FRAGMENT, COMPLEMENT C3C ALPHA' CHAIN FRAGMENT 2
 
Molecule 2 - INTEGRIN ALPHA-M
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PETM-11
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 143-337
    Gene: CD11B, CR3A, ITGAM
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: CD11 ANTIGEN-LIKE FAMILY MEMBER B, CR-3 ALPHA CHAIN, CELL SURFACE GLYCOPROTEIN MAC-1 SUBUNIT ALPHA, LEUKOCYTE ADHESION RECEPTOR MO1, NEUTROPHIL ADHERENCE RECEPTOR

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1NI2Ligand/IonNICKEL (II) ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:992 , HOH A:1419 , HOH A:1420 , HOH A:1421 , HIS B:148BINDING SITE FOR RESIDUE NI A 1301
2AC2SOFTWAREASP A:1247 , SER B:142 , SER B:144 , THR B:209 , HOH B:501 , HOH B:502BINDING SITE FOR RESIDUE NI B 401

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:1101 -A:1158

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Glu A:1138 -Lys A:1139
2Lys B:165 -Lys B:166
3Ser B:167 -Lys B:168
4Lys B:290 -Pro B:291

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4M76)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4M76)

(-) Exons   (0, 0)

(no "Exon" information available for 4M76)

(-) 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:296
                                                                                                                                                                                                                                                                                                                                         
               SCOP domains d4m76a_ A: Thio-ester containing domain (TED) from Complement C3, aka C3d or C3dg                                                                                                                                                                                                                        SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh................hhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhh.............hhhhhhhhh....hhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4m76 A  992 AMAVDAERLKHLIVTPSGAGEQNMIGMTPTVIAVHYLDETEQWEKFGLEKRQGALELIKKGYTQQLAFRQPSSAFAAFVKRAPSTWLTAYVVKVFSLAVNLIAIDSQVLCGAVKWLILEKQKPDGVFQEDAPVIHQEMIGGLRNNNEKDMALTAFVLISLQEAKDICEEQVNSLPGSITKAGDFLEANYMNLQRSYTVAIAGYALAQMGRLKGPLLNKFLTTAKDKNRWEDPGKQLYNVEATSYALLALLQLKDFDFVPPVVRWLNEQRYYGGGYGSTQATFMVFQALAQYQKDAP 1287
                                  1001      1011      1021      1031      1041      1051      1061      1071      1081      1091      1101      1111      1121      1131      1141      1151      1161      1171      1181      1191      1201      1211      1221      1231      1241      1251      1261      1271      1281      


Chain B from PDB  Type:PROTEIN  Length:179
                                                                                                                                                                                                                    
               SCOP domains d4m76b_ B: automated matches                                                                                                                                                        SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee.....hhhhhhhhhhhhhhhhhh.....eeeeeeee...eeeeehhhhhhhh.hhhhhhh.........hhhhhhhhhhhhh.hhhhh.....eeeeeee..........hhhhhhhhhhhh..eeeeee.......hhhhhhhhhhh..hhhh.eee..hhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4m76 B  132 DSDIAFLIDGSGSIIPHDFRRMKEFVSTVMEQLKKSKTLFSLMQYSEEFRIHFTFKEFQNNPNPRSLVKPITQLLGRTHTATGIRKVVRELFNITNGARKNAFKILVVITDGEKFGDPLGYEDVIPEADREGVIRYVIGVGDAFRSEKSRQELNTIASKPPRDHVFQVNNFEALKTIQN  310
                                   141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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  (2, 2)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4M76)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4M76)

(-) Gene Ontology  (58, 62)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Glu A:1138 - Lys A:1139   [ RasMol ]  
    Lys B:165 - Lys B:166   [ RasMol ]  
    Lys B:290 - Pro B:291   [ RasMol ]  
    Ser B:167 - Lys B:168   [ RasMol ]  
 

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  4m76
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  ITAM_HUMAN | P11215
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 Related Entries

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

UniProtKB/Swiss-Prot
        CO3_HUMAN | P01024: 1c3d 1ghq 1w2s 2a73 2a74 2gox 2i07 2ice 2icf 2noj 2qki 2wii 2win 2wy7 2wy8 2xqw 2xwb 2xwj 3d5r 3d5s 3g6j 3l3o 3l5n 3nms 3oed 3ohx 3oxu 3rj3 3t4a 4hw5 4hwj 4i6o 4ont 4zh1 5fo7 5fo8 5fo9 5foa 5fob 5m6w 5o32 5o35
        ITAM_HUMAN | P11215: 1a8x 1bho 1bhq 1idn 1ido 1jlm 1m1u 1mf7 1n9z 1na5 2lke 2lkj 3q3g 3qa3 4xw2

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4M76)