5DHY - JenaLib

Asymmetric Unit (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   HIV-1 REV NTD DIMERS WITH VARIABLE CROSSING ANGLES

Authors :   M. A. Dimattia, N. R. Watts, P. T. Wingfield, J. M. Grimes, D. I. Stuart, A

Date :   31 Aug 15 (Deposition) - 22 Jun 16 (Release) - 20 Jul 16 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.10

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

Keywords :   Hiv, Helical Hairpin, Rna-Binding, Nuclear Export, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. A. Dimattia, N. R. Watts, N. Cheng, R. Huang, J. B. Heymann, J. M. Grimes, P. T. Wingfield, D. I. Stuart, A. C. Steven
The Structure Of Hiv-1 Rev Filaments Suggests A Bilateral Model For Rev-Rre Assembly.
Structure V. 24 1068 2016
PubMed-ID: 27265851 | Reference-DOI: 10.1016/J.STR.2016.04.015

Molecule 1 - ANTI-REV ANTIBODY FAB SINGLE-CHAIN VARIABLE FRAGMENT, HEAVY CHAIN
	Chains	:	A, H
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

Molecule 2 - ANTI-REV ANTIBODY FAB SINGLE-CHAIN VARIABLE FRAGMENT, LIGHT CHAIN
	Chains	:	B, L
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

Molecule 3 - PROTEIN REV
	Chains	:	C, M
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	REV
	Organism Scientific	:	HUMAN IMMUNODEFICIENCY VIRUS 1
	Organism Taxid	:	11676

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

Summary Information (see also Sequences/Alignments below)

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

(no "Site" information available for 5DHY)

Asymmetric Unit

No.	Residues
1	A:22	-	A:94
2	B:23	-	B:88
3	H:22	-	H:94
4	L:23	-	L:88

Asymmetric Unit

No.	Residues
1	Thr B:7	-	Pro B:8
2	Thr C:34	-	Arg C:35
3	Thr L:7	-	Pro L:8
4	Thr M:34	-	Arg M:35

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

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

(no "Exon" information available for 5DHY)

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:117
                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee.......eeeeeee.....eeeeeeee....eeee.......eeeee...eeeeee...hhhhheeeeeeee........ee...eeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------- Transcript
                 5dhy A   1 QEQLVESGGRLVTPGTALTLTCKVSGFSLSGFWLNWVRQAPGKGLEWVGAIYRGSGSEWYASWAKGRFTISDTSTTVTLKLTSPTTEDTATYFCAADTTDNGYFTIWGPGTLVTVSS 117
                                    10        20        30        40        50        60        70        80        90       100       110

Chain B from PDB  Type:PROTEIN  Length:110
                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeeee.......eee...eeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------- Transcript
                 5dhy B   1 ELVMTQTPSSVSEPVGGTVTIKCQASQSISSWLSWYQQKPGQPPKLLIYDASNLASGVPSRFMGSGSGTEYTLTISGVQREDAATYYCLGGYPAASYRTAFGGGTELEII 110
                                    10        20        30        40        50        60        70        80        90       100       110

Chain C from PDB  Type:PROTEIN  Length:61
                                                                                             
               SCOP domains ------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------- Transcript
                 5dhy C   5 SGDSDEDLLKAVRLIKFLYQSNPPPNPEGTRQARRNRRRRWRERQRQIHSISERILSTYLG  65
                                    14        24        34        44        54        64

Chain H from PDB  Type:PROTEIN  Length:117
                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee.......eeeeeee.....eeeeeeee....eeee.......eeeee...eeeeee...hhhhheeeeeeee........ee...eeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------- Transcript
                 5dhy H   1 QEQLVESGGRLVTPGTALTLTCKVSGFSLSGFWLNWVRQAPGKGLEWVGAIYRGSGSEWYASWAKGRFTISDTSTTVTLKLTSPTTEDTATYFCAADTTDNGYFTIWGPGTLVTVSS 117
                                    10        20        30        40        50        60        70        80        90       100       110

Chain L from PDB  Type:PROTEIN  Length:110
                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeeee.......eee...eeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------- Transcript
                 5dhy L   1 ELVMTQTPSSVSEPVGGTVTIKCQASQSISSWLSWYQQKPGQPPKLLIYDASNLASGVPSRFMGSGSGTEYTLTISGVQREDAATYYCLGGYPAASYRTAFGGGTELEII 110
                                    10        20        30        40        50        60        70        80        90       100       110

Chain M from PDB  Type:PROTEIN  Length:61
                                                                                             
               SCOP domains ------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------- Transcript
                 5dhy M   5 SGDSDEDLLKAVRLIKFLYQSNPPPNPEGTRQARRNRRRRWRERQRQIHSISERILSTYLG  65
                                    14        24        34        44        54        64

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 '\|'

(no "SCOP Domain" information available for 5DHY)

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

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

Asymmetric Unit(hide GO term definitions)

Asymmetric Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 5dhy)

	Sites
(no "Sites" information available for 5dhy)

	Cis Peptide Bonds
		Thr B:7 - Pro B:8	[ RasMol ]
		Thr C:34 - Arg C:35	[ RasMol ]
		Thr L:7 - Pro L:8	[ RasMol ]
		Thr M:34 - Arg M:35	[ RasMol ]

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

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 2 PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	5dhy
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	Q76PP8_9HIV1 \| Q76PP8
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt
	REV_HV1B1 \| P04616
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	(no 'Enzyme Classificator' available)
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	Q76PP8_9HIV1 \| Q76PP8
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)
	REV_HV1B1 \| P04616
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	Q76PP8_9HIV1 \| Q76PP8	:	5dhv 5dhz
	REV_HV1B1 \| P04616	:	2x7l 5dhv 5dhx 5dhz

5dhv	5DHV IS A DIFFERENT CRYSTAL FORM, VARIABLE CROSSING ANGLES OF REV N- TERMINAL DOMAIN
5dhx	5DHX IS A DIFFERENT CRYSTAL FORM, VARIABLE CROSSING ANGLES OF REV N- TERMINAL DOMAIN

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (4, 4)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (9, 17)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File