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(-) Description

Title :  CRYSTAL STRUCTURE OF BROADLY NEUTRALIZING ANTI-HIV-1 ANTIBODY 4E10, MUTANT NPRO, WITH PEPTIDE BOUND
 
Authors :  J. M. M. Caaveiro, E. Rujas, J. L. Nieva, K. Tsumoto
Date :  20 Jan 17  (Deposition) - 05 Apr 17  (Release) - 26 Apr 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.49
Chains :  Asym./Biol. Unit :  H,L,P
Keywords :  Broadly Neutralizing Antibody, Mper, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Rujas, S. Insausti, M. Garcia-Porras, R. Sanchez-Eugenia, K. Tsumoto, J. L. Nieva, J. M. M. Caaveiro
Functional Contacts Between Mper And The Anti-Hiv-1 Broadly Neutralizing Antibody 4E10 Extend Into The Core Of The Membrane
J. Mol. Biol. V. 429 1213 2017
PubMed-ID: 28300601  |  Reference-DOI: 10.1016/J.JMB.2017.03.008
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - FAB 4E10 HEAVY CHAIN
    Chains: H
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PCOLADUET
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Variant: T7 SHUFFLE
    Expression System Vector Type: PLASMID
    Gene: IGG1
    Mutation: YES
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 2 - FAB 4E10 LIGHT CHAIN
    Chains: L
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PCOLADUET
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Variant: T7 SHUFFLE
    Expression System Vector Type: PLASMID
    Gene: IGG1
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 3 - ENVELOPE GLYCOPROTEIN GP160
    Chains: P
    Engineered: YES
    Expression System: SYNTHETIC CONSTRUCT
    Expression System Taxid: 32630
    Gene: ENV
    Organism Scientific: HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 (MAL ISOLATE)
    Organism Taxid: 11697

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : HLP

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 6)

Asymmetric/Biological Unit (5, 6)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2CL1Ligand/IonCHLORIDE ION
3GOL2Ligand/IonGLYCEROL
4P6G1Ligand/IonHEXAETHYLENE GLYCOL
5PGE1Ligand/IonTRIETHYLENE GLYCOL

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE H:174 , PRO H:175 , SER H:186 , LEU H:187 , SER H:188 , HOH H:402 , GLN L:160 , SER L:162 , SER L:176 , SER L:177 , THR L:178binding site for residue GOL H 301
2AC2SOFTWARETYR H:79 , GLU H:81 , HOH H:437binding site for residue PGE H 302
3AC3SOFTWARELYS H:213 , GLN L:11 , ARG L:18 , ALA L:19 , THR L:20 , HOH L:440binding site for residue GOL L 301
4AC4SOFTWAREARG H:43 , HOH H:577 , GLY L:9 , THR L:10 , GLN L:38 , GLY L:41 , TYR L:87 , GLN L:100 , GLY L:101 , ARG L:142 , HOH L:427 , HOH L:468 , HOH L:557binding site for residue P6G L 302
5AC5SOFTWAREARG L:45 , ALA L:59 , HOH L:403 , HOH L:595binding site for residue CL L 303
6AC6SOFTWARESER L:94 , HOH L:434 , ASN P:671 , TRP P:672 , ILE P:682 , HOH P:802binding site for residue ACT P 701

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1H:22 -H:92
2H:142 -H:208
3L:23 -L:88
4L:134 -L:194

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Phe H:148 -Pro H:149
2Glu H:150 -Pro H:151
3Ser L:7 -Pro L:8
4Tyr L:140 -Pro L:141

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5X08)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5X08)

(-) Exons   (0, 0)

(no "Exon" information available for 5X08)

(-) 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 H from PDB  Type:PROTEIN  Length:217
                                                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee........eeeeee.....eeeeeeee....eeee.hhhh..eeeeee....eeeeee...hhhhheeeeeeeeee....eeeeeeee...eeeee........eeeee....eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhhh....eeeeeehhhheeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5x08 H    1 QVQLVQSGAEVKRPGSSVTVSCKASGGSFSTYALSWVRQAPGRGLEWMGGVIPLLTITNYAPRFQGRITITADRSTSTAYLELNSLRPEDTAVYYCAREGTTPGKPIGAFAHWGQGTLVTVSSASTKGPSVFPLAPSGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEP  227
                                    10        20        30        40        50  |     59        69        79   |||  86        96   |||100J       110       120      |138       148     ||163     ||174     ||185       195    |||208       218   ||  
                                                                              52A                            82A||              100D||||||                        127|               154|||    169|      180|               200||              222|  
                                                                                                              82B|               100E|||||                         136                156||     171       182                203|               225  
                                                                                                               82C                100F||||                                             157|                                   205                    
                                                                                                                                   100G|||                                              162                                                          
                                                                                                                                    100H||                                                                                                           
                                                                                                                                     100I|                                                                                                           
                                                                                                                                      100J                                                                                                           


Chain L from PDB  Type:PROTEIN  Length:212
                                                                                                                                                                                                                                                     
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee....eeee.....eeeeeee...hhhh.eeeeee......eeee.............eeeeee..eeeeee...hhhhh.eeeeee......ee...eeeee.......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhh...eeeeeee.......eeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5x08 L    1 EIVLTQSPGTQSLSPGERATLSCRASQSVGNNKLAWYQQRPGQAPRLLIYGASSRPSGVADRFSGSGSGTDFTLTISRLEPEDFAVYYCQQYGQSLSTFGQGTKVEVKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNR  211
                                    10        20       |29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209  
                                                     27A                                                                                                                                                                                        


Chain P from PDB  Type:PROTEIN  Length:14
                                               
               SCOP domains -------------- SCOP domains
               CATH domains -------------- CATH domains
               Pfam domains -------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------- SAPs(SNPs)
                    PROSITE -------------- PROSITE
                 Transcript -------------- Transcript
                5x08 P  671 NWFDITNWLWYIKK  684
                                   680
   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 5X08)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5X08)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5X08)

(-) Gene Ontology  (32, 32)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Glu H:150 - Pro H:151   [ RasMol ]  
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  5x08
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  ENV_HV1H2 | P04578
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 Related Entries

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

UniProtKB/Swiss-Prot
        ENV_HV1H2 | P04578: 1aik 1df4 1df5 1dlb 1g9m 1gc1 1gzl 1k33 1k34 1mzi 1opn 1opt 1opw 1rzj 2cmr 2me1 2mg1 2mg2 2mg3 2ny7 2pv6 2x7r 2xra 2zzo 3d0v 3dnl 3dnn 3dno 3dro 3idx 3idy 3j70 3tyg 3vie 4jpj 4jpk 4ydv 4zto 5bn0 5c0r 5c0s 5cil 5cin 5cmu 5cmz 5cn0 5dd0 5ghw 5h0n 5hfl 5hm1 5ivx 5ka5 5ka6

(-) Related Entries Specified in the PDB File

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