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Asym./Biol. Unit  (Jmol Viewer)

(-) Description

Title :  CRYOEM STRUCTURE REFINEMENT BY INTEGRATING NMR CHEMICAL SHIFTS WITH MOLECULAR DYNAMICS SIMULATIONS
 
Authors :  J. R. Perilla
Date :  04 Feb 17  (Deposition) - 01 Mar 17  (Release) - 03 May 17  (Revision)
Method :  ELECTRON MICROSCOPY
Resolution :  5.00
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F
Keywords :  Cryo-Em, Hiv Capsid, Chemical Shift, Molecular Dynamics, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. R. Perilla, G. Zhao, M. Lu, J. Ning, G. Hou, I. L. Byeon, A. M. Gronenborn, T. Polenova, P. Zhang
Cryoem Structure Refinement By Integrating Nmr Chemical Shifts With Molecular Dynamics Simulations.
J Phys Chem B V. 121 3853 2017
PubMed-ID: 28181439  |  Reference-DOI: 10.1021/ACS.JPCB.6B13105

(-) Compounds

Molecule 1 - GAG POLYPROTEIN
    Chains: A, B, C, D, E, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 133-353
    Gene: GAG
    Mutation: YES
    Organism Scientific: HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 (NEW YORK-5 ISOLATE)
    Organism Taxid: 11698
    Synonym: PR55GAG

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABCDEF

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 5UPW)

(-) SS Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1A:198 -A:218
2B:198 -B:218
3C:198 -C:218
4D:198 -D:218
5E:198 -E:218
6F:198 -F:218

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Asn A:121 -Pro A:122
2Asn B:121 -Pro B:122
3Asn D:121 -Pro D:122
4Asn E:121 -Pro E:122

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5UPW)

(-) 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:221
                                                                                                                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee...eeee...hhhhhhhhhhhhhhhh...hhhhhhhhhh...hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh...............hhhhhhh...hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh...hhhhh......hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh.hhhhhhhhhhhh...hhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5upw A   1 PIVQNLQGQMVHQAISPRTLNAWVKVVEEKAFSPEVIPMFSALSEGATPQDLNTMLNTVGGHQAAMQMLKETINEEAAEWDRLHPVHAGPIAPGQMREPRGSDIAGTTSTLQEQIGWMTHNPPIPVGEIYKRWIILGLNKIVRMYSPTSILDIRQGPKEPFRDYVDRFYKTLRAEQASQEVKNWMTETLLVQNANPDCKTILKALGPGATLEEMMTACQGV 221
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220 


Chain B from PDB  Type:PROTEIN  Length:221
                                                                                                                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeehhheeee...hhhhhhhhhhhhhhhh...hhhhhhhhhh...hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh...............hhhhhh....hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh..hhhhh......hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.hhhhhhhhhhhh...hhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5upw B   1 PIVQNLQGQMVHQAISPRTLNAWVKVVEEKAFSPEVIPMFSALSEGATPQDLNTMLNTVGGHQAAMQMLKETINEEAAEWDRLHPVHAGPIAPGQMREPRGSDIAGTTSTLQEQIGWMTHNPPIPVGEIYKRWIILGLNKIVRMYSPTSILDIRQGPKEPFRDYVDRFYKTLRAEQASQEVKNWMTETLLVQNANPDCKTILKALGPGATLEEMMTACQGV 221
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220 


Chain C from PDB  Type:PROTEIN  Length:221
                                                                                                                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee...eeee...hhhhhhhhhhhhhhhh...hhhhhhhhhh...hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh...............hhhhhhh...hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh...hhhhh......hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.hhhhhhhhhhhh...hhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5upw C   1 PIVQNLQGQMVHQAISPRTLNAWVKVVEEKAFSPEVIPMFSALSEGATPQDLNTMLNTVGGHQAAMQMLKETINEEAAEWDRLHPVHAGPIAPGQMREPRGSDIAGTTSTLQEQIGWMTHNPPIPVGEIYKRWIILGLNKIVRMYSPTSILDIRQGPKEPFRDYVDRFYKTLRAEQASQEVKNWMTETLLVQNANPDCKTILKALGPGATLEEMMTACQGV 221
                                    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:221
                                                                                                                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeehhheeee...hhhhhhhhhhhhhhhh...hhhhhhhhhh...hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh...............hhhhhh....hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh...hhhhh......hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.hhhhhhhhhhhh...hhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5upw D   1 PIVQNLQGQMVHQAISPRTLNAWVKVVEEKAFSPEVIPMFSALSEGATPQDLNTMLNTVGGHQAAMQMLKETINEEAAEWDRLHPVHAGPIAPGQMREPRGSDIAGTTSTLQEQIGWMTHNPPIPVGEIYKRWIILGLNKIVRMYSPTSILDIRQGPKEPFRDYVDRFYKTLRAEQASQEVKNWMTETLLVQNANPDCKTILKALGPGATLEEMMTACQGV 221
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220 


Chain E from PDB  Type:PROTEIN  Length:221
                                                                                                                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeehhheeee...hhhhhhhhhhhhhhhh...hhhhhhhhhh...hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh...............hhhhhh....hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh...hhhhh......hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5upw E   1 PIVQNLQGQMVHQAISPRTLNAWVKVVEEKAFSPEVIPMFSALSEGATPQDLNTMLNTVGGHQAAMQMLKETINEEAAEWDRLHPVHAGPIAPGQMREPRGSDIAGTTSTLQEQIGWMTHNPPIPVGEIYKRWIILGLNKIVRMYSPTSILDIRQGPKEPFRDYVDRFYKTLRAEQASQEVKNWMTETLLVQNANPDCKTILKALGPGATLEEMMTACQGV 221
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220 


Chain F from PDB  Type:PROTEIN  Length:221
                                                                                                                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee...eeee...hhhhhhhhhhhhhhhh...hhhhhhhhhh...hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh...............hhhhhhh...hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh..hhhhh......hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5upw F   1 PIVQNLQGQMVHQAISPRTLNAWVKVVEEKAFSPEVIPMFSALSEGATPQDLNTMLNTVGGHQAAMQMLKETINEEAAEWDRLHPVHAGPIAPGQMREPRGSDIAGTTSTLQEQIGWMTHNPPIPVGEIYKRWIILGLNKIVRMYSPTSILDIRQGPKEPFRDYVDRFYKTLRAEQASQEVKNWMTETLLVQNANPDCKTILKALGPGATLEEMMTACQGV 221
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220
   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 5UPW)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (21, 21)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Asn A:121 - Pro A:122   [ RasMol ]  
    Asn B:121 - Pro B:122   [ RasMol ]  
    Asn D:121 - Pro D:122   [ RasMol ]  
    Asn E:121 - Pro E:122   [ RasMol ]  
 

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  5upw
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  GAG_HV1N5 | P12493
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 Related Entries

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

UniProtKB/Swiss-Prot
        GAG_HV1N5 | P12493: 1gwp 1hiw 1uph 2c55 2x2d 3gv2 4u0a 4u0b 4u0c 4u0d 4u0e 4u0f 4xfx 4xfy 4xfz 4xro 4xrq 5hgl 5hgm 5hgn 5hgo 5hgp 5irt 5jpa 5l93 5o2u

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5UPW)