4EN2 - JenaLib

Asymmetric Unit (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   HIV-1 NEF IN COMPLEX WITH MHC-I CYTOPLASMIC DOMAIN AND MU1 ADAPTIN SUBUNIT OF AP1 ADAPTOR (SECOND DOMAIN)

Authors :   X. Jia, Y. Xiong

Date :   12 Apr 12 (Deposition) - 20 Jun 12 (Release) - 25 Jul 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.58

Chains :   Asym. Unit : A,B,C,D,E,M
Biol. Unit 1: C,D,M  (1x)
Biol. Unit 2: A,B,E  (1x)

Keywords :   Human Immunodeficiency Virus 1, Hiv, Nef, Mhc-I, Antigen Presentation, Host Defense, Adaptor Protein Complex 1, Mu1 Adaptin Subunit, Sorting Motif Recognition, Clasp, Membrane Trafficking, Viral Hijacking, Viral Protein-Immune System Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   X. Jia, R. Singh, S. Homann, H. Yang, J. Guatelli, Y. Xiong
Structural Basis Of Evasion Of Cellular Adaptive Immunity B Hiv-1 Nef.
Nat. Struct. Mol. Biol. V. 19 701 2012
PubMed-ID: 22705789 | Reference-DOI: 10.1038/NSMB.2328

Molecule 1 - AP-1 COMPLEX SUBUNIT MU-1
	Chains	:	M, A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	SORTING MOTIF RECOGNITION DOMAIN
	Gene	:	AP1M1, CLTNM
	Organism Common	:	MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Synonym	:	AP-MU CHAIN FAMILY MEMBER MU1A, ADAPTOR PROTEIN COMPLEX AP-1 MU-1 SUBUNIT, ADAPTOR-RELATED PROTEIN COMPLEX 1 MU-1 SUBUNIT, CLATHRIN ASSEMBLY PROTEIN COMPLEX 1 MEDIUM CHAIN 1, CLATHRIN COAT ASSEMBLY PROTEIN AP47, CLATHRIN COAT-ASSOCIATED PROTEIN AP47, GOLGI ADAPTOR HA1/AP1 ADAPTIN MU-1 SUBUNIT, MU-ADAPTIN 1, MU1A-ADAPTIN

Molecule 2 - PROTEIN NEF
	Chains	:	B, C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	NEF
	Organism Scientific	:	HUMAN IMMUNODEFICIENCY VIRUS 1
	Organism Taxid	:	11676
	Strain	:	NL-43

Molecule 3 - MHC-I
	Chains	:	D, E
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	CYTOPLASMIC DOMAIN
	Gene	:	HLA-2
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

		1	2	3	4	5	6
Asymmetric Unit	:	A	B	C	D	E	M
Biological Unit 1 (1x)	:			C	D		M
Biological Unit 2 (1x)	:	A	B			E

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 4EN2)

(no "Site" information available for 4EN2)

(no "SS Bond" information available for 4EN2)

Asymmetric Unit

No.	Residues
1	Gly B:130	-	Pro B:131
2	Gly C:130	-	Pro C:131

(no "SAP(SNP)/Variant" information available for 4EN2)

(no "PROSITE Motif" information available for 4EN2)

(no "Exon" information available for 4EN2)

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:255
                                                                                                                                                                                                                                                                                               
               SCOP domains d4en2a_ A: automated matches                                                                                                                                                                                                                                    SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeeeeeeeeeeeee.....eeeeeeeeeeeeeee.....eeeeee.hhhhhhhh..........eeeee....hhhhhhhhh.eee....eeeeeeeeee.......eeeeeeeee....eeeeeeeeee......eeeeeeeeee.....eeeeeee...eeeee....eeeeeeeeee...eeeeeeeee.....eeeeeeee.ee.....eeeeeee......eeeeeeeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4en2 A 160 RSEGIKYRKNEVFLDVIEAVNLLVSANGNVLRSEIVGSIKMRVFLSGMPELRLGLNDKVLFDNTGRGKSKSVELEDVKFHQCVRLSRFENDRTISFIPPDGEFELMSYRLNTHVKPLIWIESVIEKHSHSRIEYMVKAKSQFKRRSTANNVEIHIPVPNDADSPKFKTTVGSVKWVPENSEIVWSVKSFPGGKEYLMRAHFGLPKPPISVKFEIPYFTTSGIQVRYLKIIEKSGYQALPWVRYITQNGDYQLRTQ 423
                                   169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359   ||  378       388       398       408       418     
                                                                                                                                                                                                                                     363|                                                  
                                                                                                                                                                                                                                      373

Chain B from PDB  Type:PROTEIN  Length:149
                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh.......ee..........hhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhh.......................eeeee.hhhhhhhhhhh........eeeee.hhhhh.hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4en2 B   6 SKSSVIGWPAVRERMRRAEPAEEVGFPVTPQVPLRPMTYKAAVDLSHFLKEKGGLEGLIHSQRRQDILDLWIYHTQGYFPDWQNYTPGPGVRYPLTFGWCYKLVPVEPDKVEEANKGENDPEREVLEWRFDSRLAFHHVARELHPEYFK 204
                                    15        25||      72        82        92       102       112       122       132       142       152       175       185       195         
                                               26|                                                                                              161|                             
                                                64                                                                                               175

Chain C from PDB  Type:PROTEIN  Length:133
                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh..ee.ee.....ee..........hhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhh.......................eeeee...eeeee.hhhhh.hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4en2 C   9 SVIGWPAVRERMRRAEWLEAQEEEEVGFPVTPQVPLRPMTYKAAVDLSHFLKEKGGLEGLIHSQRRQDILDLWIYHTQGYFPDWQNYTPGPGVRYPLTFGWCYKLVPVEVLEWRFDSRLAFHHVARELHPEYF 203
                                    18     || 60        70        80        90       100       110       120       130       140       180       190       200   
                                          24|                                                                                        148|                        
                                           57                                                                                         179

Chain D from PDB  Type:PROTEIN  Length:12
                                            
               SCOP domains ------------ SCOP domains
               CATH domains ------------ CATH domains
               Pfam domains ------------ Pfam domains
         Sec.struct. author ..ee........ Sec.struct. author
                 SAPs(SNPs) ------------ SAPs(SNPs)
                    PROSITE ------------ PROSITE
                 Transcript ------------ Transcript
                 4en2 D 319 SYSQAAGSDSAQ 330
                                   328

Chain E from PDB  Type:PROTEIN  Length:18
                                                  
               SCOP domains ------------------ SCOP domains
               CATH domains ------------------ CATH domains
               Pfam domains ------------------ Pfam domains
         Sec.struct. author .......ee....hhhhh Sec.struct. author
                 SAPs(SNPs) ------------------ SAPs(SNPs)
                    PROSITE ------------------ PROSITE
                 Transcript ------------------ Transcript
                 4en2 E 314 DRKGGSYSQAAGSDSAQG 331
                                   323

Chain M from PDB  Type:PROTEIN  Length:256
                                                                                                                                                                                                                                                                                                
               SCOP domains d4en2m_ M: automated matches                                                                                                                                                                                                                                     SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeeeeeeeeeeeeee.....eeeeeeeeeeeeeee.....eeeeee.hhhhhhhh..........eeeee....hhhhhhhhh..ee....eeeeeeeeee.......eeeeeeeeeee..eeeeeeeeee......eeeeeeeeee.....eeeeeee...eeeee....eeeeeeeeee...eeeeeeeee....eeeeeeee.ee.....eeeeeee......eeeeeeeeee...eee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4en2 M 158 SWRSEGIKYRKNEVFLDVIEAVNLLVSANGNVLRSEIVGSIKMRVFLSGMPELRLGLNDKVLFDNTGRGKSKSVELEDVKFHQCVRLSRFENDRTISFIPPDGEFELMSYRLNTHVKPLIWIESVIEKHSHSRIEYMVKAKSQFKRRSTANNVEIHIPVPNDADSPKFKTTVGSVKWVPENSEIVWSVKSFPGGKEYLMRAHFGLKPPISVKFEIPYFTTSGIQVRYLKIIEKSGYQALPWVRYITQNGDYQLRTQ 423
                                   167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357    || 377       387       397       407       417      
                                                                                                                                                                                                                                      362|                                                  
                                                                                                                                                                                                                                       373

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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: Common fold of diphtheria toxin/transcription factors/cytochrome f (364)

Superfamily: Second domain of Mu2 adaptin subunit (ap50) of ap2 adaptor (10)

Family: automated matches (3)

Protein domain: automated matches (3)

Mouse (Mus musculus) [TaxId: 10090] (2)

1a	d4en2a_	A:
1b	d4en2m_	M:

(no "CATH Domain" information available for 4EN2)

(no "Pfam Domain" information available for 4EN2)

Asymmetric Unit(hide GO term definitions)

Asymmetric Unit
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	Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 4en2)

	Sites
(no "Sites" information available for 4en2)

	Cis Peptide Bonds
		Gly B:130 - Pro B:131	[ RasMol ]
		Gly C:130 - Pro C:131	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

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	Q90VU7_9HIV1 \| Q90VU7
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4emz	SE-MET DERIVATIVE OF THE SAME PROTEIN COMPLEX

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (1, 2)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (69, 76)

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