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(-) Description

Title :  CRYSTAL STRUCTURE OF THE SARS CORONAVIRUS NSP14-NSP10 COMPLEX WITH FUNCTIONAL LIGAND SAM
 
Authors :  Y. Y. Ma, L. J. Wu, R. G. Zhang, Z. H. Rao
Date :  26 Jun 15  (Deposition) - 15 Jul 15  (Release) - 12 Aug 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.20
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Nsp14, Nsp10, Exoribonuclease, Methyltransferase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Y. Ma, L. J. Wu, N. Shaw, Y. Gao, J. Wang, Y. N. Sun, Z. Y. Lou, L. M. Yan, R. G. Zhang, Z. H. Rao
Structural Basis And Functional Analysis Of The Sars Coronavirus Nsp14-Nsp10 Complex
Proc. Natl. Acad. Sci. Usa V. 112 9436 2015
PubMed-ID: 26159422  |  Reference-DOI: 10.1073/PNAS.1508686112

(-) Compounds

Molecule 1 - NON-STRUCTURAL PROTEIN 10
    Chains: A, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Common: SARS-COV
    Organism Scientific: HUMAN SARS CORONAVIRUS
    Organism Taxid: 227859
    Synonym: NSP10
 
Molecule 2 - GUANINE-N7 METHYLTRANSFERASE
    Chains: B, D
    EC Number: 2.1.1.-, 3.1.13.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Common: SARS-COV
    Organism Scientific: HUMAN SARS CORONAVIRUS
    Organism Taxid: 227859
    Synonym: NSP14

 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, 14)

Asymmetric Unit (3, 14)
No.NameCountTypeFull Name
1MG2Ligand/IonMAGNESIUM ION
2SAM2Ligand/IonS-ADENOSYLMETHIONINE
3ZN10Ligand/IonZINC ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2SAM1Ligand/IonS-ADENOSYLMETHIONINE
3ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2SAM1Ligand/IonS-ADENOSYLMETHIONINE
3ZN-1Ligand/IonZINC ION

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWARECYS A:74 , CYS A:77 , HIS A:83 , CYS A:90binding site for residue ZN A 201
02AC2SOFTWARECYS A:117 , CYS A:120 , CYS A:128 , CYS A:130binding site for residue ZN A 202
03AC3SOFTWARECYS B:207 , CYS B:210 , CYS B:226 , HIS B:229binding site for residue ZN B 601
04AC4SOFTWAREHIS B:257 , CYS B:261 , HIS B:264 , CYS B:279binding site for residue ZN B 602
05AC5SOFTWARECYS B:452 , CYS B:477 , CYS B:484 , HIS B:487binding site for residue ZN B 603
06AC6SOFTWAREASP B:90 , ALA B:187 , GLU B:191binding site for residue MG B 604
07AC7SOFTWAREGLY B:333 , PRO B:335 , ASP B:352 , ALA B:353 , GLN B:354 , LEU B:366 , PHE B:367 , TYR B:368 , TRP B:385 , ASN B:386 , CYS B:387binding site for residue SAM B 605
08AC8SOFTWARECYS C:74 , CYS C:77 , HIS C:83 , CYS C:90binding site for residue ZN C 201
09AC9SOFTWARECYS C:117 , CYS C:120 , CYS C:128 , CYS C:130binding site for residue ZN C 202
10AD1SOFTWARECYS D:207 , CYS D:210 , CYS D:226 , HIS D:229binding site for residue ZN D 601
11AD2SOFTWAREHIS D:257 , CYS D:261 , HIS D:264 , CYS D:279binding site for residue ZN D 602
12AD3SOFTWARECYS D:452 , CYS D:477 , CYS D:484 , HIS D:487binding site for residue ZN D 603
13AD4SOFTWAREASP D:90 , GLU D:191binding site for residue MG D 604
14AD5SOFTWARETRP D:292 , GLY D:333 , PRO D:335 , ASP D:352 , ALA D:353 , GLN D:354 , LEU D:366 , PHE D:367 , TYR D:368 , TRP D:385 , ASN D:386 , ASN D:388binding site for residue SAM D 605

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5C8T)

(-) Cis Peptide Bonds  (14, 14)

Asymmetric Unit
No.Residues
1Ser A:0 -Ala A:1
2Tyr A:126 -Gly A:127
3Ala B:1 -Glu B:2
4Gly B:17 -Leu B:18
5Gly B:156 -Leu B:157
6Ile B:299 -Gly B:300
7Cys B:414 -Asp B:415
8Gly B:481 -Ala B:482
9Thr C:47 -His C:48
10Ala C:54 -Ile C:55
11Cys C:120 -Gly C:121
12Glu D:2 -Asn D:3
13Gly D:17 -Leu D:18
14Cys D:414 -Asp D:415

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5C8T)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5C8T)

(-) Exons   (0, 0)

(no "Exon" information available for 5C8T)

(-) 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:133
                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhh.hhhhhhhhhhhh.....................ee........eeeeehhhhhhhhhhh...............eeeee.hhh.hhhhhhhhh................. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5c8t A  -1 GSAGNATEVPANSTVLSFCAFAVDPAKAYKDYLASGGQPITNCVKMLCTHTGTGQAITVTPEANMDQESFGGASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLRNTVCTVCGMWKGYGCSCD 131
                                     8        18        28        38        48        58        68        78        88        98       108       118       128   


Chain B from PDB  Type:PROTEIN  Length:514
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............................hhh.ee..ee.............eee...................hhhhhhhh...eeeeeeeeee........eeeeeeee....eee...eeeee....eeeee.......hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh......eeee..hhhhhhhhhhhh................eee....eee.........ee...eeee.hhhh...hhhhhhhhhh.......hhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhh..eeeee..............eeeeee...........ee...hhhhhh......eeeee..........eeeeee........eee.....eee.....eee...hhhhhh..ee...............................hhhhhhhhhhhhhhhhhhhhh.eeeee.....hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5c8t B   1 AENVTGLFKDCSKIITGLHPTQAPTHLSVDIKFKTEGLCVDIPGIPKDMTYRRLISMMGFKMNYQVNGYPNMFITREEAIRHVRAWIGFDVEGCHATRDAVGTNLPLQLGFSTGVNLVAVPTGYVDTENNTEFTRVNAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTLKGLSDRVVFVLWAHGFELTSMKYFVKIGPERTCCLCDKRATCFSTSSDTYACWNHSVGFDYVYNPFMIDVQQWGFTGNLQSNHDQHCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWSVEYPIIGDELRVNSACRKVQHMVVKSALLADKFPVLHDIGNPKAIKCVPQAEVEWKFYDAQPCSDKAYKIEELFYSYATHHDKFTDGVCLFWNCNVDRYPANAIVCRFDTRVLSNLNLPGCDGGSLYVNKHAFHTPAFDKSAFTNLKQLPFFYYSDSPCEYVPLKSATCITRCNLGGAVCRHHANEYRQYLDAYNMMISAGFSLWIYKQFDTYNLWNTFTR 525
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450  ||   471       481       491       501       511       521    
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              453|                                                            
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               465                                                            


Chain C from PDB  Type:PROTEIN  Length:133
                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhh..hhhhhhhhhhhh...............................eeeee.hhhhhhhhh................eeeee.hhhhhhhhhhhhh.ee....ee........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5c8t C  -1 GSAGNATEVPANSTVLSFCAFAVDPAKAYKDYLASGGQPITNCVKMLCTHTGTGQAITVTPEANMDQESFGGASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLRNTVCTVCGMWKGYGCSCD 131
                                     8        18        28        38        48        58        68        78        88        98       108       118       128   


Chain D from PDB  Type:PROTEIN  Length:514
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........................hhhhhhhh.ee..ee.............eee...................hhhhhhhh...eeeeeeeeeee.......eeeeeeee....eee...eeeee....eeeee..ee...hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh......eeee.hhhhhhhhhhhhh................eee....eee.........ee...eeee........hhhhhhhhhh.......hhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhhhh..eeeee..............eeeee.................hhhhhh......eeeee..........eeeeee........eee.....eee.....eee...hhhhhh..ee....ee..............ee.........hhhhhhhhhhhhhhhhhhhhh.eeeee....hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5c8t D   1 AENVTGLFKDCSKIITGLHPTQAPTHLSVDIKFKTEGLCVDIPGIPKDMTYRRLISMMGFKMNYQVNGYPNMFITREEAIRHVRAWIGFDVEGCHATRDAVGTNLPLQLGFSTGVNLVAVPTGYVDTENNTEFTRVNAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTLKGLSDRVVFVLWAHGFELTSMKYFVKIGPERTCCLCDKRATCFSTSSDTYACWNHSVGFDYVYNPFMIDVQQWGFTGNLQSNHDQHCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWSVEYPIIGDELRVNSACRKVQHMVVKSALLADKFPVLHDIGNPKAIKCVPQAEVEWKFYDAQPCSDKAYKIEELFYSYATHHDKFTDGVCLFWNCNVDRYPANAIVCRFDTRVLSNLNLPGCDGGSLYVNKHAFHTPAFDKSAFTNLKQLPFFYYSDSPCEYVPLKSATCITRCNLGGAVCRHHANEYRQYLDAYNMMISAGFSLWIYKQFDTYNLWNTFTR 525
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450  ||   471       481       491       501       511       521    
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              453|                                                            
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               465
   Legend:   → Mismatch (orange background)
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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  (0, 0)

(no "SCOP Domain" information available for 5C8T)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5C8T)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5C8T)

(-) Gene Ontology  (64, 64)

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  Cis Peptide Bonds
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    Glu D:2 - Asn D:3   [ RasMol ]  
    Gly B:156 - Leu B:157   [ RasMol ]  
    Gly B:17 - Leu B:18   [ RasMol ]  
    Gly B:481 - Ala B:482   [ RasMol ]  
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 Related Entries

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UniProtKB/Swiss-Prot
        R1AB_CVHSA | P0C6X7: 1o5s 1p76 1p9t 1pa5 1puk 1q1x 1q2w 1qz8 1sxf 1uj1 1uk2 1uk3 1uk4 1uw7 1wof 1ysy 1z1i 1z1j 2a5a 2a5i 2a5k 2acf 2ahm 2aj5 2alv 2amd 2amq 2bx3 2bx4 2c3s 2d2d 2duc 2fav 2fe8 2fyg 2g1f 2g9t 2ga6 2gdt 2gri 2gt7 2gt8 2gtb 2gx4 2gz7 2gz8 2gz9 2h2z 2h85 2hob 2hsx 2idy 2jzd 2jze 2jzf 2k87 2op9 2ozk 2pwx 2q6g 2qc2 2qcy 2qiq 2rhb 2rnk 2v6n 2vj1 2xyq 2xyr 2xyv 2z3c 2z3d 2z3e 2z94 2z9g 2z9j 2z9k 2z9l 3d62 3e9s 3ebn 3r24 4tww 4twy 4wy3 4zuh 5b6o 5c5n 5c5o 5c8s 5c8u 5e6j 5f22 5tl6 5tl7

(-) Related Entries Specified in the PDB File

5c8s 5c8u