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(-) Description

Title :  CRYSTAL STRUCTURE OF CD4-MIMETIC MINIPROTEIN M48U1 IN COMPLEX WITH HIV-1 YU2 GP120 IN P212121 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 :  1.78
Chains :  Asym. Unit :  A,G,M,R
Biol. Unit 1:  A,G,M  (1x)
Biol. Unit 2:  A,G,R  (1x)
Keywords :  Glycoprotein, Hiv-1 Attachment Glycoprotein, Cd4-Mimetic Miniprotein, Cd4, 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, G
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Common: HUMAN
    Expression System Taxid: 9606
    Gene: GP120
    Organism Scientific: HUMAN IMMUNODEFICIENCY VIRUS 1
    Organism Taxid: 11676
    Strain: YU2
 
Molecule 2 - CD4-MIMETIC MINIPROTEIN M48U1
    Chains: M, R
    Engineered: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : AGMR
Biological Unit 1 (1x): AGM 
Biological Unit 2 (1x): AG R

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (8, 37)

Asymmetric Unit (8, 37)
No.NameCountTypeFull Name
1DPR2Mod. Amino AcidD-PROLINE
2EDO1Ligand/Ion1,2-ETHANEDIOL
3IPA8Ligand/IonISOPROPYL ALCOHOL
4MPT2Mod. Amino AcidBETA-MERCAPTOPROPIONIC ACID
5NAG18Ligand/IonN-ACETYL-D-GLUCOSAMINE
6NH22Mod. Amino AcidAMINO GROUP
7SO42Ligand/IonSULFATE ION
8U2X2Mod. Amino AcidO-(CYCLOHEXYLMETHYL)-L-TYROSINE
Biological Unit 1 (8, 33)
No.NameCountTypeFull Name
1DPR1Mod. Amino AcidD-PROLINE
2EDO1Ligand/Ion1,2-ETHANEDIOL
3IPA8Ligand/IonISOPROPYL ALCOHOL
4MPT1Mod. Amino AcidBETA-MERCAPTOPROPIONIC ACID
5NAG18Ligand/IonN-ACETYL-D-GLUCOSAMINE
6NH21Mod. Amino AcidAMINO GROUP
7SO42Ligand/IonSULFATE ION
8U2X1Mod. Amino AcidO-(CYCLOHEXYLMETHYL)-L-TYROSINE
Biological Unit 2 (8, 33)
No.NameCountTypeFull Name
1DPR1Mod. Amino AcidD-PROLINE
2EDO1Ligand/Ion1,2-ETHANEDIOL
3IPA8Ligand/IonISOPROPYL ALCOHOL
4MPT1Mod. Amino AcidBETA-MERCAPTOPROPIONIC ACID
5NAG18Ligand/IonN-ACETYL-D-GLUCOSAMINE
6NH21Mod. Amino AcidAMINO GROUP
7SO42Ligand/IonSULFATE ION
8U2X1Mod. Amino AcidO-(CYCLOHEXYLMETHYL)-L-TYROSINE

(-) Sites  (31, 31)

Asymmetric Unit (31, 31)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREPRO A:76 , ASP A:78 , HOH A:696 , HOH A:888BINDING SITE FOR RESIDUE IPA A 510
02AC2SOFTWAREASN A:262 , SER A:446 , ASN A:448 , NAG A:505 , NAG A:509BINDING SITE FOR RESIDUE IPA A 511
03AC3SOFTWAREHIS A:72 , ILE A:423 , LYS A:432 , MET A:434BINDING SITE FOR RESIDUE IPA A 512
04AC4SOFTWARELYS A:421 , GLN A:422 , ILE A:423 , HOH A:880 , HOH A:929 , HOH A:1001BINDING SITE FOR RESIDUE SO4 A 513
05AC5SOFTWAREALA G:73 , HOH G:1014BINDING SITE FOR RESIDUE IPA G 509
06AC6SOFTWAREVAL G:200 , HOH G:873BINDING SITE FOR RESIDUE IPA G 510
07AC7SOFTWARESER G:446 , NAG G:502 , NAG G:508BINDING SITE FOR RESIDUE IPA G 511
08AC8SOFTWAREGLU A:268 , NAG A:514 , HOH G:899BINDING SITE FOR RESIDUE EDO G 512
09AC9SOFTWARELYS G:421 , GLN G:422 , ILE G:423 , HOH G:875 , HOH G:1011 , HOH G:1022BINDING SITE FOR RESIDUE SO4 G 513
10BC1SOFTWAREGLY M:14 , LEU M:15 , LEU M:16 , HOH M:214 , SER R:12BINDING SITE FOR RESIDUE IPA A 515
11BC2SOFTWAREGLY A:367 , ARG R:9BINDING SITE FOR RESIDUE IPA A 516
12BC3SOFTWAREASN A:276 , THR A:278 , ASN A:279 , HOH A:658 , HOH A:799 , HOH A:804 , HOH A:876 , LYS G:46 , ASN G:92 , HOH G:647BINDING SITE FOR MONO-SACCHARIDE NAG A 502 BOUND TO ASN A 234
13BC4SOFTWAREASN A:234 , THR A:236 , SER A:274 , HOH A:744 , HOH A:997BINDING SITE FOR MONO-SACCHARIDE NAG A 503 BOUND TO ASN A 234
14BC5SOFTWAREASN A:229 , ASN A:241 , HOH A:844 , THR G:240BINDING SITE FOR MONO-SACCHARIDE NAG A 504 BOUND TO ASN A 241
15BC6SOFTWAREGLU A:211 , PRO A:212 , ASN A:262 , CYS A:445 , SER A:446 , SER A:447 , NAG A:509 , IPA A:511 , HOH A:704 , HOH A:758 , HOH A:791 , HOH A:815 , HOH A:993BINDING SITE FOR MONO-SACCHARIDE NAG A 505 BOUND TO ASN A 262
16BC7SOFTWAREASN A:356 , LYS A:357 , HOH A:1011BINDING SITE FOR MONO-SACCHARIDE NAG A 501 BOUND TO ASN A 276
17BC8SOFTWAREGLU A:268 , GLU A:269 , ASN A:289 , GLU A:290 , GLU G:351 , HOH G:879BINDING SITE FOR MONO-SACCHARIDE NAG A 506 BOUND TO ASN A 289
18BC9SOFTWAREASN A:295 , LEU A:333 , ASN A:413 , ARG A:444 , HOH A:823 , HOH A:847 , HOH A:962 , PRO G:79 , ASN G:80BINDING SITE FOR MONO-SACCHARIDE NAG A 507 BOUND TO ASN A 295
19CC1SOFTWAREASN A:386 , THR A:388 , HOH A:970 , HOH A:1034 , HOH A:1038BINDING SITE FOR MONO-SACCHARIDE NAG A 508 BOUND TO ASN A 386
20CC2SOFTWAREARG A:252 , ASN A:262 , ASN A:448 , NAG A:505 , IPA A:511 , HOH A:702 , HOH A:708 , HOH A:714 , HOH A:768 , HOH A:995 , HOH A:996BINDING SITE FOR MONO-SACCHARIDE NAG A 509 BOUND TO ASN A 448
21CC3SOFTWAREASN G:234 , THR G:236 , SER G:274 , EDO G:512 , HOH G:849BINDING SITE FOR MONO-SACCHARIDE NAG A 514 BOUND TO ASN G 234
22CC4SOFTWARETHR A:240 , ASN G:229 , ASN G:241BINDING SITE FOR MONO-SACCHARIDE NAG G 501 BOUND TO ASN G 241
23CC5SOFTWAREGLU G:211 , PRO G:212 , LEU G:261 , ASN G:262 , CYS G:445 , SER G:446 , SER G:447 , NAG G:508 , IPA G:511 , HOH G:677 , HOH G:699 , HOH G:753 , HOH G:1039BINDING SITE FOR MONO-SACCHARIDE NAG G 502 BOUND TO ASN G 241
24CC6SOFTWARELYS A:46 , ASN A:92 , HOH A:895 , ASN G:276 , THR G:278 , ASN G:279 , HOH G:797 , HOH G:826 , HOH G:853 , HOH G:870 , HOH G:872BINDING SITE FOR MONO-SACCHARIDE NAG G 503 BOUND TO ASN G 262
25CC7SOFTWAREGLU A:351 , GLU G:268 , GLU G:269 , ASN G:289 , GLU G:290 , GLN G:344BINDING SITE FOR MONO-SACCHARIDE NAG G 504 BOUND TO ASN G 276
26CC8SOFTWAREPRO A:79 , ASN A:80 , ASN G:295 , ASN G:332 , LEU G:333 , ASN G:413 , ARG G:444 , HOH G:828 , HOH G:998BINDING SITE FOR MONO-SACCHARIDE NAG G 505 BOUND TO ASN G 289
27CC9SOFTWAREASN G:386 , THR G:388 , HOH G:640 , HOH G:724 , HOH G:902 , HOH G:931 , HOH G:1031BINDING SITE FOR MONO-SACCHARIDE NAG G 506 BOUND TO ASN G 295
28DC1SOFTWAREASN G:394 , ARG G:397 , HOH G:1037BINDING SITE FOR MONO-SACCHARIDE NAG G 507 BOUND TO ASN G 386
29DC2SOFTWAREASN G:262 , SER G:291 , ASN G:448 , NAG G:502 , IPA G:511 , HOH G:651 , HOH G:681 , HOH G:759 , HOH G:856 , HOH G:916BINDING SITE FOR MONO-SACCHARIDE NAG G 508 BOUND TO ASN G 394
30DC3SOFTWARELYS A:207 , ARG A:440 , IPA A:515 , HOH A:774 , HOH A:793 , HOH A:827 , ALA G:60 , VAL G:255 , ALA G:281 , SER G:365 , GLY G:366 , GLY G:367 , ASP G:368 , GLU G:370 , ILE G:371 , SER G:375 , PHE G:382 , ASN G:425 , MET G:426 , TRP G:427 , GLU G:429 , VAL G:430 , GLY G:472 , GLY G:473 , MET G:475 , HOH G:611 , HOH G:669 , HOH G:675 , HOH M:204 , HOH M:205 , HOH M:206 , HOH M:207 , HOH M:208 , HOH M:209 , HOH M:210 , HOH M:211 , HOH M:212 , HOH M:220 , HOH M:222 , LYS R:11 , SER R:12 , GLY R:14BINDING SITE FOR CHAIN M OF CD4-MIMETIC MINIPROTEIN M48U1
31DC4SOFTWAREALA A:60 , VAL A:255 , ALA A:281 , SER A:365 , GLY A:366 , GLY A:367 , ASP A:368 , GLU A:370 , ILE A:371 , SER A:375 , PHE A:382 , ASN A:425 , MET A:426 , TRP A:427 , GLU A:429 , GLY A:472 , GLY A:473 , MET A:475 , IPA A:515 , IPA A:516 , HOH A:603 , HOH A:607 , HOH A:624 , LYS G:207 , ARG G:440 , HOH G:809 , HOH G:953 , LYS M:11 , SER M:12 , GLY M:14 , HOH R:201 , HOH R:204 , HOH R:206 , HOH R:207 , HOH R:208 , HOH R:209 , HOH R:210 , HOH R:213 , HOH R:214 , HOH R:215 , HOH R:216 , HOH R:219 , HOH R:220 , HOH R:221 , HOH R:223BINDING SITE FOR CHAIN R OF CD4-MIMETIC MINIPROTEIN M48U1

(-) SS Bonds  (20, 20)

Asymmetric 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
8G:54 -G:74
9G:119 -G:205
10G:218 -G:247
11G:228 -G:239
12G:296 -G:331
13G:378 -G:445
14G:385 -G:418
15M:1 -M:19
16M:6 -M:24
17M:10 -M:26
18R:1 -R:19
19R:6 -R:24
20R:10 -R:26

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Thr G:462 -Asn G:463

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4JZW)

(-) 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:336
                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..ee.....eeee.......hhhhhhhhhheee......eeee....eeee...hhhhhhhhhhhhhhhhhhh...eeee..eeee.............eee....eeeeee.......eeee..eeee.............eee.........eeee.........eeeeeeeeeeeeeee......eeeeeeehhhhhhhhhhhhhhhhhhhh...eeee......hhhhhheeeee..eeeee..............eeeeeeeee.eee......eee........eeeeeeeeeeeeee....eeeeee...hhhhhhhhhhh.eeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4jzw A  44 VWKEATTTLFCASDAKAYDTEVHNVWATHACVPTDPNPQEVKLENVTENFNMWKNNMVEQMHEDIISLWDQSLKPCVKLTGGSVITQACPKVSFEPIPIHYCAPAGFAILKCNDKKFNGTGPCTNVSTVQCTHGIRPVVSTQLLLNGSLAEEEIVIRSENFTNNAKTIIVQLNESVVINCTRPNNDIRQAHCNLSKTQWENTLEQIAIKLKEQFGNNKTIIFNPSSGGDPEIVTHSFNCGGEFFYCNSTQLFTWNDTRGRNITLPCRIKQIINMWQEVGKAMYAPPIRGQIRCSSNITGLLLTRDGGGTEIFRPGGGDMRDNWRSELYKYKVVKIE 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       412       422       432       442       452      |466       476       486      
                                                                                                          124|                                                                                                    301|                                                                     397|                                             459|                            
                                                                                                           198                                                                                                     325                                                                      411                                              464                            


Chain G from PDB  Type:PROTEIN  Length:339
                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee.....eeee.......hhhhhhhhhheee.......ee.....eeee...hhhhhhhhhhhhhhhhhhh...eeee..eeee............eeee....eeeeee.......eeee..eeee.............eee.........eeee.........eeeeeeeeeeeeeee......eeeeeeehhhhhhhhhhhhhhhhhhhh...eeee......hhhhhheeeee..eeeee.hhhhhh........eeeeeeeee.eee......eee........eeeeeeeeeeeeee......eeeeee...hhhhhhhhhhh.eeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jzw G  44 VWKEATTTLFCASDAKAYDTEVHNVWATHACVPTDPNPQEVKLENVTENFNMWKNNMVEQMHEDIISLWDQSLKPCVKLTGGSVITQACPKVSFEPIPIHYCAPAGFAILKCNDKKFNGTGPCTNVSTVQCTHGIRPVVSTQLLLNGSLAEEEIVIRSENFTNNAKTIIVQLNESVVINCTRPNNDIRQAHCNLSKTQWENTLEQIAIKLKEQFGNNKTIIFNPSSGGDPEIVTHSFNCGGEFFYCNSTQLFTWNDTRTGRNITLPCRIKQIINMWQEVGKAMYAPPIRGQIRCSSNITGLLLTRDGGTNGTEIFRPGGGDMRDNWRSELYKYKVVKIE 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       411       421       431       441       451       463       473       483         
                                                                                                          124|                                                                                                    301|                                                                     397|                                              459|                              
                                                                                                           198                                                                                                     325                                                                      410                                               462                              


Chain M from PDB  Type:PROTEIN  Length:28
                                                            
               SCOP domains ---------------------------- SCOP domains
               CATH domains ---------------------------- CATH domains
               Pfam domains ---------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh..eeeee..eeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------- SAPs(SNPs)
                    PROSITE ---------------------------- PROSITE
                 Transcript ---------------------------- Transcript
                 4jzw M   1 xNLHFCQLRCKSLGLLGRCAxTyCACVx  28
                            |       10        20| |    |
                            1-MPT              21-DPR  |
                                                 23-U2X|
                                                      28-NH2


Chain R from PDB  Type:PROTEIN  Length:28
                                                            
               SCOP domains ---------------------------- SCOP domains
               CATH domains ---------------------------- CATH domains
               Pfam domains ---------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhh...eeeee..eeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------- SAPs(SNPs)
                    PROSITE ---------------------------- PROSITE
                 Transcript ---------------------------- Transcript
                 4jzw R   1 xNLHFCQLRCKSLGLLGRCAxTyCACVx  28
                            |       10        20| |    |
                            |                  21-DPR  |
                            1-MPT                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 4JZW)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (21, 21)

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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4JZW)