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(-) Description

Title :  ELECTRON CRYO-MICROSCOPY OF GRAPEVINE FANLEAF VIRUS COMPLEX WITH NANOBODY
 
Authors :  C. Hemmer, I. Orlov, L. Ackerer, A. Marmonier, K. Hleibieh, C. Schmitt-Keichinger, E. Vigne, S. Gersch, V. Komar, L. Belval, F. Be B. Monsion, P. Bron, O. Lemaire, B. Lorber, J. Y. Sgro, C. Gutierrez, S. Muyldermans, G. Demangeat, B. P. Klaholz, C. Ritzenthaler
Date :  22 Nov 15  (Deposition) - 20 Jan 16  (Release) - 13 Apr 16  (Revision)
Method :  ELECTRON MICROSCOPY
Resolution :  2.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (60x)
Keywords :  Virus, Nanobody, Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Hemmer, I. Orlov, L. Ackerer, A. Marmonier, K. Hleibieh, C. Schmitt-Keichinger, E. Vigne, S. Gersch, V. Komar, L. Belval, F. Berthold, B. Monsion, P. Bron, O. Lemaire, B. Lorber, J. Y. Sgro, C. Gutierrez, S. Muyldermans, G. Demangeat, B. P. Klaholz, C. Ritzenthaler
Structural Basis Of Nanobody-Mediated Plant Virus Resistance And Vector Transmission Revealed By Cryo-Em.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - NANOBODY
    Chains: A
    Organism Common: CAMEL
    Organism Scientific: CAMELUS DROMEDARIUS
    Organism Taxid: 9838
 
Molecule 2 - GRAPEVINE FANLEAF VIRUS
    Chains: B
    Fragment: UNP RESIDUES 606-1109
    Organism Scientific: GRAPEVINE FANLEAF VIRUS
    Organism Taxid: 12274
    Synonym: P2,2B-MP, 2C-CP

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (60x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 5FOJ)

(-) Sites  (0, 0)

(no "Site" information available for 5FOJ)

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1B:14 -B:134

(-) Cis Peptide Bonds  (11, 11)

Asymmetric Unit
No.Residues
1Ala A:24 -Ser A:25
2Gly A:26 -Asp A:27
3Phe A:29 -Ser A:30
4Ser A:30 -Gly A:31
5Asn A:52 -Ser A:53
6Thr A:91 -Ala A:92
7Ala A:101 -Ile A:102
8Gly B:211 -Thr B:212
9Trp B:255 -Asn B:256
10Gly B:313 -Pro B:314
11Ser B:318 -Gly B:319

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5FOJ)

(-) 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:131
                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee.............eeee.........ee..............ee................eeeeee....eeeeee...................hhhhhhh....hhhhh............. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5foj A   1 QVQLQESGGGSVQVGGSLRVACAASGDTFSGYLAAWFRQAPGKGREGVAAINSKRHTTSYADSVKGRFTISKDNADNIMYLEMNSLKPEDTAIYYCAAADAIGLAEYWSTPTLSAARYKYWGQGTQVTVSS 131
                                    10        20        30        40        50        60        70        80        90       100       110       120       130 


Chain B from PDB  Type:PROTEIN  Length:504
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeeee........eeeeeehhhhhhhh.hhhhhhhhhhh....eeeeeee.........eeeeeee......hhhhh..hhhhhhhh.eeeee......eeeeehhhhh..............eeeeeeee.........eeeeeeee..............ee.................eee.......eee.................hhhhhhhhh.......eeeeeee......eeeeeeeee......hhhhhhhh..eee....eeee.......................eeeeeeeeeee........eeeeeeeeee..............eeeeeee......ee.....................hhhhhhhhhh.eeeeeeeeee..ee..hhhhh..eeeeeee............eeee.hhh.eeeeeee......ee.........eeeeee.hhh.eeeeeeeeee....eee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5foj B   1 GLAGRGVIYIPKDCQANRYLGTLNIRDMISDFKGVQYEKWITAGLVMPTFKIVIRLPANAFTGLTWVMSFDAYNRITSRITASADPVYTLSVPHWLIHHKLGTFSCEIDYGELCGHAMWFKSTTFESPRLHFTCLTGNNKELAADWQAVVELYAELEEATSFLGKPTLVFDPGVFNGKFQFLTCPPIFFDLTAVTALRSAGLTLGQVPMVGTTKVYNLNSTLVSCVLGMGGTVRGRVHICAPIFYSIVLWVVSEWNGTTMDWNELFKYPGVYVEEDGSFEVKIRSPYHRTPARLLAGQSQRDMSSLNFYAIAGPIAPSGETAQLPIVVQIDEIVRPDLSLPSFEDDYFVWVDFSEFTLDKEEIEIGSRFFDFTSNTCRVSMGENPFAAMIACHGLHSGVLDLKLQWSLNTEFGKSSGSVTITKLVGDKAMGLDGPSHVFAIQKLEGTTELLVGNFAGANPNTRFSLYSRWMAIKLDQAKSIKVLRVLCKPRPGFSFYGRTSFPV 504
                                    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       460       470       480       490       500
   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 5FOJ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)

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  Sites
(no "Sites" information available for 5foj)
 
  Cis Peptide Bonds
    Ala A:101 - Ile A:102   [ RasMol ]  
    Ala A:24 - Ser A:25   [ RasMol ]  
    Asn A:52 - Ser A:53   [ RasMol ]  
    Gly A:26 - Asp A:27   [ RasMol ]  
    Gly B:211 - Thr B:212   [ RasMol ]  
    Gly B:313 - Pro B:314   [ RasMol ]  
    Phe A:29 - Ser A:30   [ RasMol ]  
    Ser A:30 - Gly A:31   [ RasMol ]  
    Ser B:318 - Gly B:319   [ RasMol ]  
    Thr A:91 - Ala A:92   [ RasMol ]  
    Trp B:255 - Asn B:256   [ RasMol ]  
 
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  POL2_GFLV | P18474
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 Related Entries

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UniProtKB/Swiss-Prot
        POL2_GFLV | P18474: 2y26 4v5t 4v5w

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