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(-) Description

Title :  TERNARY COMPLEX OF HUMAN COMPLEMENT C5 WITH ORNITHODOROS MOUBATA OMCI AND RHIPICEPHALUS APPENDICULATUS RACI1
 
Authors :  M. M. Jore, S. Johnson, S. M. Lea
Date :  04 Jan 16  (Deposition) - 30 Mar 16  (Release) - 18 May 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.12
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Complement, Inflammation, Inhibitor, Tick, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. M. Jore, S. Johnson, D. Sheppard, N. M. Barber, Y. I. Li, M. A. Nunn, H. Elmlund, S. M. Lea
Structural Basis For Therapeutic Inhibition Of Complement C5.
Nat. Struct. Mol. Biol. V. 23 378 2016
PubMed-ID: 27018802  |  Reference-DOI: 10.1038/NSMB.3196

(-) Compounds

Molecule 1 - COMPLEMENT C5
    Chains: B
    Fragment: UNP RESIDUES 19-674
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: CHAINS A AND B ARE THE PRODUCT OF A SINGLE GENE THAT IS PROCESSED INTO TWO CHAINS THAT REMAIN COVALENTLY LINKED VIA A DISULPHIDE.
    Synonym: C3 AND PZP-LIKE ALPHA-2-MACROGLOBULIN DOMAIN-CONTAINING PROTEIN 4
 
Molecule 2 - COMPLEMENT C5
    Chains: A
    Fragment: UNP RESIDUES 679-1676
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: CHAINS A AND B ARE THE PRODUCT OF A SINGLE GENE THAT IS PROCESSED INTO TWO CHAINS THAT REMAIN COVALENTLY LINKED VIA A DISULPHIDE.
    Synonym: C3 AND PZP-LIKE ALPHA-2-MACROGLOBULIN DOMAIN-CONTAINING PROTEIN 4
 
Molecule 3 - COMPLEMENT INHIBITOR
    Chains: C
    Engineered: YES
    Expression System: KLUYVEROMYCES LACTIS
    Expression System Taxid: 28985
    Fragment: UNP RESIDUES 19-168
    Gene: CI
    Mutation: YES
    Organism Common: SOFT TICK
    Organism Scientific: ORNITHODOROS MOUBATA
    Organism Taxid: 6938
 
Molecule 4 - RHIPICEPHALUS APPENDICULATUS RACI1
    Chains: D
    Engineered: YES
    Expression System: ESCHERICHIA COLI K-12
    Expression System Plasmid: PET-M14
    Expression System Taxid: 83333
    Expression System Variant: SHUFFLE T7
    Expression System Vector Type: PLASMID
    Organism Scientific: RHIPICEPHALUS APPENDICULATUS
    Organism Taxid: 34631
    Other Details: FIRST 3 RESIDUES ARE THE REMNANT OF THE HISTIDINE-TAG. MATURE SEQUENCE BEGINS EEVK.

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1CYS1Mod. Amino AcidCYSTEINE
2NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:700 , CYS A:704 , ARG A:751binding site for residue CYS A 2101
2AC2SOFTWARESER A:860 , ASN A:909 , ASN A:911 , ASN B:398 , GLU B:400binding site for Poly-Saccharide residues NAG A 2102 through NAG A 2103 bound to ASN A 911

(-) SS Bonds  (21, 21)

Asymmetric/Biological Unit
No.Residues
1A:698 -A:724
2A:699 -A:731
3A:704 -A:2101
4A:711 -A:732
5A:856 -A:883
6A:866 -A:1527
7A:1101 -A:1159
8A:1375 -A:1505
9A:1405 -A:1474
10A:1520 -A:1525
11A:1532 -A:1606
12A:1553 -A:1676
13A:1654 -A:1657
14B:567 -A:810
15B:634 -B:669
16C:24 -C:146
17C:56 -C:168
18C:118 -C:147
19D:14 -D:38
20D:19 -D:40
21D:34 -D:55

(-) Cis Peptide Bonds  (10, 10)

Asymmetric/Biological Unit
No.Residues
1Tyr B:59 -Pro B:60
2His B:473 -Lys B:474
3Val B:535 -Pro B:536
4Ser B:576 -Pro B:577
5Gly A:996 -Ile A:997
6Leu A:1180 -Pro A:1181
7Asn A:1221 -Pro A:1222
8Lys A:1515 -Ile A:1516
9Glu C:28 -Pro C:29
10Val D:49 -Pro D:50

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5HCE)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5HCE)

(-) Exons   (0, 0)

(no "Exon" information available for 5HCE)

(-) 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:983
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhh.....hhhhhhhh......hhhhhhh....hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh.....ee...........eeee..eeeeeee.....eeeeeeeeeee..eeee...eeeee...eeeeee....ee...eeeeeeeeee.....eeeeeee.....eee.............eee...eeeeeeeeeee...eeeeeeeeeee..eeeeeeeeeeee...eeeeeeeeeee...........eeee..............eeeeeee...hhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhh.hhhhh..hhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh....................hhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh....hhhhhhhhhhhhhh.eee.....eee................hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhh.....eeeeeeee......eeeeee........ee......eeeee......eeeeeeeeeee.........eeeeeeee.....eeeeeeee.............eeeeee....eeehhhhhhhhhh.......eeeee..eeeeee........eeeeeeeee...ee....eeeeeee..eeeeeeeeee....................................hhhhhh.......eeeeeeeeeeeee..eeeeeeeeeeeeee.........eeeeeee............eeeeee...eeeee..eeeeeee.....eeee........hhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5hce A  679 LQKKIEEIAAKYKHSVVKKCCYDGACVNNDETCEQRAARISLGPRCIKAFTECCVVASQLRANISHKDMQLGRLHMKTLLPVSKPEIRSYFPESWLWEVHLVPRRKQLQFALPDSLTTWEIQGVGISNTGICVADTVKAKVFKDVFLEMNIPYSVVRGEQIQLKGTVYNYRTSGMQFCVKMSAVEGICTSESPVIKSSKCVRQKVEGSSSHLVTFTVLPLEIGLHNINFSLETWFGKEILVKTLRVVPEGVKRESYSGVTLDPRGIYGTISRRKEFPYRIPLDLVPKTEIKRILSVKGLLVGEILSAVLSQEGINILTHLPKGSAEAELMSVVPVFYVFHYLETGNHWNIFHSDPLIEKQKLKKKLKEGMLSIMSYRNADYSYSVWKGGSASTWLTAFALRVLGQVNKYVEQNQNSICNSLLWLVENYQLDNGSFKENSQYQPIKLQGTLPVEARENSLYLTAFTVIGIRKAFDICPLVKIDTALIKADNFLLENTLPAQSTFTLAISAYALSLGDKTHPQFRSIVSALKREALVKGNPPIYRFWKDNLQHKDSSVPNTGTARMVETTAYALLTSLNLKDINYVNPVIKWLSEEQRYGGGFYSTQDTINAIEGLTEYSLLVKQLRLSMDIDVSYKHKGALHNYKMTDKNFLGRPVEVLLNDDLIVSTGFGSGLATVHVTTVVHKTSTSEEVCSFYLKIDTQDIEAKRIVACASYKPSREESSSGSSHAVMDISLPTGISANEEDLKALVEGVDQLFTDYQIKDGHVILQLNSIPSSDFLCVRFRIFELFEVGFLSPATFTVYEYHRPDKQCTMFYSTSNIKIQKVCEGAACKCVEADCGQMQEELDLTISAETRKQTACKPEIAYAYKVSITSITVENVFVKYKATLLDIYKTGEAVAEKDSEITFIKKVTCTNAELVKGRQYLIMGKEALQIKYNFSFRYIYPLDSLTWIEYWPRDTTCSSCQAFLANLDEFAEDIFLNGCC 2101
                                   688       698       708       718       728       738       748       758       768       778       788       798       808       818       828       838       848       858       868    || 883       893       903       913       923       933       943       953       963       973       983       993      1003      1013      1023      1033      1043      1053      1063      1073      1083      1093      1103      1113      1123      1133      1143      1153      1163      1173      1183      1193      1203      1213      1223      1233      1243      1253      1263      1273      1283      1293      1303      1313      1323      1333      1343      1353      1363      1373      1383    ||1404      1414      1424      1434      1444      1454      1464      1474      1484      1494      1504      1514      1524      1534      1544      1554      1564      1574      1584      1594      1604      1614      1624      1634      1644      1654      1664      1674 ||
                                                                                                                                                                                                                            873|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         1388|                                                                                                                                                                                                                                                                                1676|
                                                                                                                                                                                                                             879                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          1400                                                                                                                                                                                                                                                                                 2101


Chain B from PDB  Type:PROTEIN  Length:647
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee..ee...eeeeeeeee.....eeeeeeeee......eeeeeeeee......eeeeeee.hhhhh........eeeeeeee...eeeeeeeee....eeeeee...ee....ee.eeeeee..........eeeeee.....eeeeeee.....eee...ee.......eeeeeeeee......eeeeeeee.ee....eeeeeee...ee.......eeeeeeeee...ee..eeeeeeeeeee........eee.....eeeee..eeeeeehhhhhh..............eeeeeeeeee.....eeeeeeeeeee.....eeee.....ee.....eeeeeeee..........eeeeeeeeee....eee...eeee......eeeeee.....eeeeeeeeee...........eeeeeeee.......eeeee............eeeeeeeee..hhhhh.eeeeeeee..eeeeeeeee.......eeeeee.hhhhh.eeeeeeeeee......eeeeeeeeee........eeeeee..........eeeeeeee...eeeeeeeee.hhhh..hhhhhhh............hhhhhhhhh.eeeee................... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5hce B   20 EQTYVISAPKIFRVGASENIVIQVYGYTEAFDATISIKSYPDKKFSYSSGHVHLSSENKFQNSAILTIQPKQLPGGQNPVSYVYLEVVSKHFSKSKRMPITYDNGFLFIHTDKPVYTPDQSVKVRVYSLNDDLKPAKRETVLTFIDPEGSEVDMVEEIDHIGIISFPDFKIPSNPRYGMWTIKAKYKEDFSTTGTAYFEVKEYVLPHFSVSIEPEYNFIGYKNFKNFEITIKARYFYNKVVTEADVYITFGIREDLKDDQKEMMQTAMQNTMLINGIAQVTFDSETAVKELSYYSLEDLNNKYLYIAVTVIESTGGFSEEAEIPGIKYVLSPYKLNLVATPLFLKPGIPYPIKVQVKDSLDQLVGGVPVTLNAQTIDVNQETSDLDPSKSVTRVDDGVASFVLNLPSGVTVLEFNVKTDAPDLPEENQAREGYRAIAYSSLSQSYLYIDWTDNHKALLVGEHLNIIVTPKSPYIDKITHYNYLILSKGKIIHFGTREKFSDASYQSINIPVTQNMVPSSRLLVYYIVTGEQTAELVSDSVWLNIEEKCGNQLQVHLSPDADAYSPGQTVSLNMATGMDSWVALAAVDSAVYGLERVFQFLEKSDLGCGAGGGLNNANVFHLAGLTFLTNANADDSQENDEPCKEILR  674
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579       589       599       609 ||    627       637       647       657       667       
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         611|                                                      
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          620                                                      


Chain C from PDB  Type:PROTEIN  Length:148
                                                                                                                                                                                     
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhhhhhh..eeeeee......eeeeeee.......eeeeeeeeee..eeeeeeeeeeee..eeeeee..eeeeeeeeee.....eeeeee.....eeeeeee...eehhhhhhhhhhhhhhhh.....hhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5hce C   21 ESDCTGSEPVDAFQAFSEGKEAYVLVRSTDPKARDCLKGEPAGEKQDNTLPVMMTFKQGTDWASTDWTFTLDGAKVTATLGQLTQNREVVYDSQSHHCHVDKVEKEVPDYEMWMLDAGGLEVEVECCRQKLEELASGRNQMYPHLKDC  168
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160        


Chain D from PDB  Type:PROTEIN  Length:47
                                                                                
               SCOP domains ----------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------- Pfam domains
         Sec.struct. author ......eeeee.....eee.......eee.........eeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------- PROSITE
                 Transcript ----------------------------------------------- Transcript
                5hce D   13 QCVNATCERKLDALGNAVITKCPQGCLCVVRGASNIVPANGTCFQLA   59
                                    22        32        42        52
   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 5HCE)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5HCE)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5HCE)

(-) Gene Ontology  (29, 29)

Asymmetric/Biological Unit(hide GO term definitions)

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  A0A158RFT5_R | A0A158RFT5
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 Related Entries

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

UniProtKB/Swiss-Prot
        CO5_HUMAN | P01031: 1cfa 1kjs 1xwe 3cu7 3hqa 3hqb 3kls 3km9 3prx 3pvm 4a5w 4e0s 4p39 4uu9 5b4p 5b71 5hcc 5hcd 5i5k
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(-) Related Entries Specified in the PDB File

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