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(-) Description

Title :  CRYSTAL STRUCTURE OF CD4-MIMETIC MINIPROTEIN M48U1 IN COMPLEX WITH HIV-1 YU2 GP120 IN C2221 SPACE GROUP
 
Authors :  P. Acharya, P. D. Kwong
Date :  03 Apr 13  (Deposition) - 12 Jun 13  (Release) - 10 Jul 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.49
Chains :  Asym./Biol. Unit :  A,R
Keywords :  Hiv-1 Attachment Protein Gp120, Hiv-1 Envelope, Viral Protein- Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Acharya, T. S. Luongo, M. K. Louder, K. Mckee, Y. Yang, Y. Do Kwon, J. R. Mascola, P. Kessler, L. Martin, P. D. Kwong
Structural Basis For Highly Effective Hiv-1 Neutralization By Cd4-Mimetic Miniproteins Revealed By 1. 5 A Cocrystal Structure Of Gp120 And M48U1.
Structure V. 21 1018 2013
PubMed-ID: 23707685  |  Reference-DOI: 10.1016/J.STR.2013.04.015

(-) Compounds

Molecule 1 - HIV-1 YU2 GP120 GLYCOPROTEIN
    Chains: A
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Common: HUMAN
    Expression System Plasmid: PVRC8400
    Expression System Taxid: 9606
    Expression System Vector Type: PLASMID
    Gene: GP120
    Organism Scientific: HUMAN IMMUNODEFICIENCY VIRUS 1
    Organism Taxid: 11676
    Strain: YU2
 
Molecule 2 - CD4-MIMETIC MINIPROTEIN M48U1
    Chains: R
    Engineered: YES
    Other Details: DERIVED FROM SCYLLATOXIN (A SCORPION TOXIN) BY TRANSPLANTING THE GP120-INTERACTIVDERIVED FROM SCYLLATOXIN (A SCORPION TOXIN) BY TRANSPLANTING THE GP120-INTERACTIVE REGION OF CD4 ONTO THE SCYLLATOXIN SCAFFOLD,E REGION OF CD4 ONTO THE SCYLLATOXIN SCAFFOLD,
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AR

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (8, 24)

Asymmetric/Biological Unit (8, 24)
No.NameCountTypeFull Name
1DPR1Mod. Amino AcidD-PROLINE
2FLC1Ligand/IonCITRATE ANION
3IPA5Ligand/IonISOPROPYL ALCOHOL
4MPT1Mod. Amino AcidBETA-MERCAPTOPROPIONIC ACID
5NA6Ligand/IonSODIUM ION
6NAG8Ligand/IonN-ACETYL-D-GLUCOSAMINE
7NH21Mod. Amino AcidAMINO GROUP
8U2X1Mod. Amino AcidO-(CYCLOHEXYLMETHYL)-L-TYROSINE

(-) Sites  (21, 21)

Asymmetric Unit (21, 21)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREVAL A:372 , THR A:373 , ASN A:386 , SER A:387 , HOH A:713BINDING SITE FOR RESIDUE NA A 509
02AC2SOFTWAREALA A:73 , VAL A:75 , MET A:434BINDING SITE FOR RESIDUE IPA A 510
03AC3SOFTWAREHOH A:690BINDING SITE FOR RESIDUE IPA A 511
04AC4SOFTWAREASN A:262 , SER A:446 , ASN A:448 , NAG A:508BINDING SITE FOR RESIDUE IPA A 512
05AC5SOFTWARETRP A:45 , LEU A:86 , GLU A:91BINDING SITE FOR RESIDUE IPA A 513
06AC6SOFTWAREVAL A:254 , SER A:256 , LEU A:260 , LEU A:261 , HOH A:852BINDING SITE FOR RESIDUE NA A 514
07AC7SOFTWARESER A:364 , HOH A:713 , HOH A:784BINDING SITE FOR RESIDUE NA A 515
08AC8SOFTWAREHIS A:66 , TRP A:112 , PHE A:210 , PRO A:253 , HOH A:604BINDING SITE FOR RESIDUE NA A 516
09AC9SOFTWAREPHE A:210 , PRO A:212 , ASN A:377 , NAG A:504 , HOH A:604 , HOH A:621BINDING SITE FOR RESIDUE NA A 517
10BC1SOFTWAREILE A:109 , ASP A:113 , GLU A:429 , HOH A:875BINDING SITE FOR RESIDUE NA A 518
11BC2SOFTWAREPRO A:369 , LYS A:421 , HOH A:901 , HOH A:952BINDING SITE FOR RESIDUE IPA A 519
12BC3SOFTWAREHIS A:72 , GLN A:114 , ARG A:327 , ARG A:419 , ILE A:420 , LYS A:421 , GLN A:422 , ILE A:423 , HOH A:780 , HOH A:850BINDING SITE FOR RESIDUE FLC A 520
13BC4SOFTWAREASN A:234 , THR A:236 , SER A:274 , HOH A:672BINDING SITE FOR MONO-SACCHARIDE NAG A 502 BOUND TO ASN A 234
14BC5SOFTWARELYS A:85 , ASN A:229 , ASN A:241BINDING SITE FOR MONO-SACCHARIDE NAG A 503 BOUND TO ASN A 241
15BC6SOFTWAREGLU A:211 , ASN A:262 , CYS A:445 , SER A:446 , SER A:447 , NAG A:508 , NA A:517 , HOH A:607 , HOH A:645 , HOH A:650 , HOH A:858BINDING SITE FOR MONO-SACCHARIDE NAG A 504 BOUND TO ASN A 262
16BC7SOFTWAREVAL A:44 , LYS A:46 , ASN A:92 , ASN A:276 , THR A:278 , ASN A:279 , HOH A:657 , HOH A:683 , HOH A:817 , HOH A:856BINDING SITE FOR MONO-SACCHARIDE NAG A 501 BOUND TO ASN A 276
17BC8SOFTWAREGLU A:268 , GLU A:269 , ILE A:270 , ASN A:289 , GLU A:290 , GLN A:344 , LYS A:348 , GLU A:351 , HOH A:634 , HOH A:789 , HOH A:921 , HOH A:927BINDING SITE FOR MONO-SACCHARIDE NAG A 505 BOUND TO ASN A 289
18BC9SOFTWAREPRO A:79 , ASN A:80 , ASN A:295 , LEU A:333 , ASN A:413 , ARG A:444 , HOH A:735 , HOH A:768BINDING SITE FOR MONO-SACCHARIDE NAG A 506 BOUND TO ASN A 295
19CC1SOFTWAREASN A:386 , THR A:388 , HOH A:673 , HOH A:766BINDING SITE FOR MONO-SACCHARIDE NAG A 507 BOUND TO ASN A 386
20CC2SOFTWARESER A:291 , ASN A:448 , NAG A:504 , IPA A:512 , HOH A:622 , HOH A:670BINDING SITE FOR MONO-SACCHARIDE NAG A 508 BOUND TO ASN A 448
21CC3SOFTWARELYS A:207 , SER A:209 , VAL A:255 , SER A:365 , GLY A:366 , GLY A:367 , ASP A:368 , GLU A:370 , ILE A:371 , SER A:375 , PHE A:376 , PHE A:382 , ASN A:425 , MET A:426 , TRP A:427 , GLU A:429 , VAL A:430 , GLY A:472 , GLY A:473 , MET A:475 , HOH A:606 , HOH A:613 , HOH A:788 , HOH A:859 , HOH A:883 , HOH R:101 , HOH R:102 , HOH R:103 , HOH R:104 , HOH R:106 , HOH R:107 , HOH R:109 , HOH R:110 , HOH R:111 , HOH R:112 , HOH R:113 , HOH R:115 , HOH R:116 , HOH R:117BINDING SITE FOR CHAIN R OF CD4-MIMETIC MINIPROTEIN M48U1

(-) SS Bonds  (10, 10)

Asymmetric/Biological Unit
No.Residues
1A:54 -A:74
2A:119 -A:205
3A:218 -A:247
4A:228 -A:239
5A:296 -A:331
6A:378 -A:445
7A:385 -A:418
8R:1 -R:19
9R:6 -R:24
10R:10 -R:26

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4JZZ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4JZZ)

(-) 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:336
                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..ee.....eeee.......hhhhhhhhhheee......eee.....eeee...hhhhhhhhhhhhhhhhhhh...eeee..eeee.............eee....eeeeee.......eeee..eeee.............eee.........eee..........eeeeeeeeeeeeeee......eeeeeeehhhhhhhhhhhhhhhhhhhh...eeee......hhhhhheeeee..eeeee.hhhhh.......eeeeeeeee.eee......eee........eeeeeeeeeeeeee.....eeeeee...hhhhhhhhhhh.eeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4jzz A  44 VWKEATTTLFCASDAKAYDTEVHNVWATHACVPTDPNPQEVKLENVTENFNMWKNNMVEQMHEDIISLWDQSLKPCVKLTGGSVITQACPKVSFEPIPIHYCAPAGFAILKCNDKKFNGTGPCTNVSTVQCTHGIRPVVSTQLLLNGSLAEEEIVIRSENFTNNAKTIIVQLNESVVINCTRPNNDIRQAHCNLSKTQWENTLEQIAIKLKEQFGNNKTIIFNPSSGGDPEIVTHSFNCGGEFFYCNSTQLFTWNDTGRNITLPCRIKQIINMWQEVGKAMYAPPIRGQIRCSSNITGLLLTRDGGNGTEIFRPGGGDMRDNWRSELYKYKVVKIE 492
                                    53        63        73        83        93       103       113       123||     206       216       226       236       246       256       266       276       286       296    || 329       339       349       359       369       379       389      |413       423       433       443       453     ||466       476       486      
                                                                                                          124|                                                                                                    301|                                                                    396|                                             459|                             
                                                                                                           198                                                                                                     325                                                                     411                                              463                             


Chain R from PDB  Type:PROTEIN  Length:28
                                                            
               SCOP domains ---------------------------- SCOP domains
               CATH domains ---------------------------- CATH domains
               Pfam domains ---------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh..eeee..eeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------- SAPs(SNPs)
                    PROSITE ---------------------------- PROSITE
                 Transcript ---------------------------- Transcript
                 4jzz R   1 xNLHFCQLRCKSLGLLGRCAxTyCACVx  28
                            |       10        20| |    |
                            1-MPT              21-DPR  |
                                                 23-U2X|
                                                      28-NH2
   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 4JZZ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (21, 21)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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UniProtKB/Swiss-Prot
        ENV_HV1Y2 | P35961: 1g9n 1rzk 1yyl 1yym 2i5y 2i60 2ny7 2qad 3hi1 3tgq 4dvr 4jo3 4jzw 4k0a 4ka2 4laj 4r4f 4rqs 4rwy 5a7x 5a8h

(-) Related Entries Specified in the PDB File

4jzw 'CRYSTAL STRUCTURE OF CD4-MIMETIC MINIPROTEIN M48U1 IN COMPLEX WITH HIV-1 YU2 GP120 IN P212121 SPACE GROUP
4k0a