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(-) Description

Title :  CRYSTAL STRUCTURE OF A TGEV CORONAVIRUS SPIKE FRAGMENT IN COMPLEX WITH THE TGEV NEUTRALIZING MONOCLONAL ANTIBODY 1AF10
 
Authors :  J. Reguera, C. Santiago, G. Mudgal, D. Ordono, L. Enjuanes, J. M. Casasn
Date :  08 May 12  (Deposition) - 22 Aug 12  (Release) - 22 Aug 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B,E  (1x)
Biol. Unit 2:  C,D,F  (1x)
Keywords :  Beta-Barrel, Immunoglobulin, Virus Entry, Virus Neutralization, Cellular Receptor, Aminopeptidase N, Glycosylation, Virus Membrane, Viral Protein-Immune System Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Reguera, C. Santiago, G. Mudgal, D. Ordono, L. Enjuanes, J. M. Casasnovas
Structural Bases Of Coronavirus Attachment To Host Aminopeptidase N And Its Inhibition By Neutralizing Antibodies.
Plos Pathog. V. 8 02859 2012
PubMed-ID: 22876187  |  Reference-DOI: 10.1371/JOURNAL.PPAT.1002859

(-) Compounds

Molecule 1 - MONOCLONAL ANTIBODY 1AF10, HEAVY CHAIN
    Cell: HYBRIDOMA
    Chains: A, C
    Engineered: YES
    Fragment: FAB
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Other Details: FAB FRAGMENT PREPARED BY PAPAIN DIGESTION
 
Molecule 2 - MONOCLONAL ANTIBODY 1AF10, LIGHT CHAIN
    Cell: HYBRIDOMA
    Chains: B, D
    Engineered: YES
    Fragment: FAB
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Other Details: FAB FRAGMENT PREPARED BY PAPAIN DIGESTION
 
Molecule 3 - SPIKE PROTEIN
    Chains: E, F
    Engineered: YES
    Expression System: CRICETULUS GRISEUS
    Expression System Cell Line: CHO LEC 3.2.8.1
    Expression System Common: CHINESE HAMSTER
    Expression System Plasmid: PBJ5-GS
    Expression System Taxid: 10029
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 481-650
    Gene: S
    Organism Scientific: TGEV VIRULENT PURDUE
    Organism Taxid: 398812
    Strain: SC11

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): AB  E 
Biological Unit 2 (1x):   CD F

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 11)

Asymmetric Unit (2, 11)
No.NameCountTypeFull Name
1ACY2Ligand/IonACETIC ACID
2NAG9Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 1 (2, 5)
No.NameCountTypeFull Name
1ACY1Ligand/IonACETIC ACID
2NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 2 (2, 6)
No.NameCountTypeFull Name
1ACY1Ligand/IonACETIC ACID
2NAG5Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN E:516 , THR E:518 , TYR E:561 , NAG E:702 , SER F:508 , PHE F:509BINDING SITE FOR RESIDUE NAG E 701
02AC2SOFTWARENAG E:701BINDING SITE FOR RESIDUE NAG E 702
03AC3SOFTWAREASP E:520 , GLY E:522 , LEU E:536 , ASN E:538 , NAG E:704BINDING SITE FOR RESIDUE NAG E 703
04AC4SOFTWAREPHE E:575 , NAG E:703BINDING SITE FOR RESIDUE NAG E 704
05AC5SOFTWARESER E:508 , PHE E:509 , TYR E:510 , ASN F:516 , THR F:518 , TYR F:561 , HIS F:563 , NAG F:702BINDING SITE FOR RESIDUE NAG F 701
06AC6SOFTWARETYR E:510 , HIS F:563 , NAG F:701BINDING SITE FOR RESIDUE NAG F 702
07AC7SOFTWAREASP F:520 , GLY F:522 , LEU F:536 , ASN F:538 , PHE F:575 , NAG F:704BINDING SITE FOR RESIDUE NAG F 703
08AC8SOFTWARENAG F:703BINDING SITE FOR RESIDUE NAG F 704
09AC9SOFTWAREASN F:578BINDING SITE FOR RESIDUE NAG F 705
10BC1SOFTWAREGLN B:37 , ARG B:39 , ARG B:45 , PRO B:59 , HOH B:401BINDING SITE FOR RESIDUE ACY B 301
11BC2SOFTWAREGLN D:37 , ARG D:39 , ARG D:45 , PRO D:59 , HOH D:401BINDING SITE FOR RESIDUE ACY D 301

(-) SS Bonds  (14, 14)

Asymmetric Unit
No.Residues
1A:22 -A:96
2A:149 -A:204
3B:23 -B:88
4B:134 -B:194
5C:22 -C:96
6C:149 -C:204
7D:23 -D:88
8D:134 -D:194
9E:552 -E:611
10E:566 -E:579
11E:594 -E:621
12F:552 -F:611
13F:566 -F:579
14F:594 -F:621

(-) Cis Peptide Bonds  (16, 16)

Asymmetric Unit
No.Residues
1Gly A:142 -Ser A:143
2Phe A:155 -Pro A:156
3Glu A:157 -Pro A:158
4Trp A:197 -Pro A:198
5Ser B:7 -Pro B:8
6Trp B:94 -Pro B:95
7Tyr B:140 -Pro B:141
8Cys C:137 -Gly C:138
9Ser C:143 -Ser C:144
10Phe C:155 -Pro C:156
11Trp C:197 -Pro C:198
12Ser D:7 -Pro D:8
13Trp D:94 -Pro D:95
14Tyr D:140 -Pro D:141
15Pro E:653 -Arg E:654
16Arg F:630 -Thr F:631

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4F2M)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4F2M)

(-) Exons   (0, 0)

(no "Exon" information available for 4F2M)

(-) 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:214
                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee......eeeeeeee.....eeeeeee.........hhhhh..eeeee.hhh.eeeeee...hhhhheeeeeeeeee..............eeeee........eeee.......eeeeeeeeee.....eeee.hhh.....ee...ee....eeeeeeeee...........eeeee...eeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4f2m A   1 QVQLQQSGPELVKPGASVKISCKASGYAFSSSWMNWVKQRPGQGLEWIGRIYPGDGETNYSEKFKGKATLTADKSSSTAYMHLSSLTSVDSAVYFCARGGYRYDPYYAMDYWGQGTSVTVSSAKTTAPSVYPLAPTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKI 219
                                    10        20        30        40        50        60        70        80        90       100       110       120       130    || 145       155       165       175       185       195       205       215    
                                                                                                                                                                135|                                                                              
                                                                                                                                                                 141                                                                              


Chain B from PDB  Type:PROTEIN  Length:213
                                                                                                                                                                                                                                                     
               SCOP domains d4f2mb1 B:1-107 automated matches                                                                          d4f2mb2 B:108-213 automated matches                                                                        SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.......eeeeee......eeeee...ee.......eeeee...eeeeee...hhhhh.eeeeee......ee...eeeee.......eeeee..hhhhhhh....eeeeee......eeeeeee.........eeee...........eeeee............eeeeeee..eeeee........ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4f2m B   1 DILLTQSPAILSVSPGERVSLSCRASQSIGTSIHWYQQRTNGSPRPLIKYASESISGIPSRFSGSGSGTDFTLNINSVESEDIADYFCQQTDSWPTTFGAGTKLELKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNE 213
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210   


Chain C from PDB  Type:PROTEIN  Length:220
                                                                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee......eee.......eeeeee....eeeeee...hhhhheeeeeee.................eeeee........eeeee............eeeeeeeee.....eeee........eee...eee..eeeeeeeee............eeeee...eeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4f2m C   1 QVQLQQSGPELVKPGASVKISCKASGYAFSSSWMNWVKQRPGQGLEWIGRIYPGDGETNYSEKFKGKATLTADKSSSTAYMHLSSLTSVDSAVYFCARGGYRYDPYYAMDYWGQGTSVTVSSAKTTAPSVYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIE 220
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220


Chain D from PDB  Type:PROTEIN  Length:211
                                                                                                                                                                                                                                                   
               SCOP domains d4f2md1 D:1-107 automated matches                                                                          d4f2md2 D:108-211 automated matches                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee..eeee.....eeeeee........eeeeee......eeeee...ee.......eeeee...eeeeee...hhhhh.eeeeee......ee...eeeee.......eeeee....hhhhh.eeeeeeeeeee....eeeeeee..eee...eeeee.........eeeeeeeeeehhhhh....eeeeeee..eeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4f2m D   1 DILLTQSPAILSVSPGERVSLSCRASQSIGTSIHWYQQRTNGSPRPLIKYASESISGIPSRFSGSGSGTDFTLNINSVESEDIADYFCQQTDSWPTTFGAGTKLELKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR 211
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210 


Chain E from PDB  Type:PROTEIN  Length:148
                                                                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeeeeeeeee.....eee....eee.........eee.....eeeeeeeeeee...........hhhhh.eeeeee.............eeeeeeeee.........eeeeee....eeeeee.eeeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4f2m E 507 PSFYTHTIVNITIDLGMKRSGYGQPIASTLSNITLPMQDNNTDVYCIRSDQFSVYVHSTCKSSLWDNIFKRNCTDVLDATAVIKTGTCPFSFDKLNNYLTFNKFCLSLSPVGANCKFDVAARTRTNEQVVRSLYVIYEEGDNIVLVPR 654
                                   516       526       536       546       556       566       576       586       596       606       616       626       636       646        


Chain F from PDB  Type:PROTEIN  Length:148
                                                                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeeeeeeeee.....eee....eee..........ee.....eeeeeeeeeee........ee........eee................eeeeeeee.......eeeeeeee....eeeeeeeeeeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4f2m F 507 PSFYTHTIVNITIDLGMKRSGYGQPIASTLSNITLPMQDNNTDVYCIRSDQFSVYVHSTCKSSLWDNIFKRNCTDVLDATAVIKTGTCPFSFDKLNNYLTFNKFCLSLSPVGANCKFDVAARTRTNEQVVRSLYVIYEEGDNIVLVPR 654
                                   516       526       536       546       556       566       576       586       596       606       616       626       636       646
   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, 4)

Asymmetric Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4F2M)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4F2M)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)

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  Cis Peptide Bonds
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 Related Entries

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4f5c