3IK5 - JenaLib

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Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Title :   SIVMAC239 NEF IN COMPLEX WITH TCR ZETA ITAM 1 POLYPEPTIDE (A63-R80)

Authors :   W. M. Kim, A. B. Sigalov, L. J. Stern

Date :   05 Aug 09 (Deposition) - 02 Feb 10 (Release) - 28 Mar 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.05

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D  (1x)
Biol. Unit 2: A,B  (1x)
Biol. Unit 3: C,D  (1x)

Keywords :   Protein-Protein Complex, Cell Membrane, Lipoprotein, Membrane, Myristate, Viral Immunoevasion, Virulence, Disulfide Bond, Host- Virus Interaction, Phosphoprotein, Receptor, Transmembrane, Viral Protein-Antiviral Protein Complex, Viral Protein-Signaling Protein Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   W. M. Kim, A. B. Sigalov, L. J. Stern
Pseudo-Merohedral Twinning And Noncrystallographic Symmetry In Orthorhombic Crystals Of Sivmac239 Nef Core Domain Bound To Different-Length Tcrzeta Fragments.
Acta Crystallogr. , Sect. D V. 66 163 2010
PubMed-ID: 20124696 | Reference-DOI: 10.1107/S090744490904880X

Molecule 1 - PROTEIN NEF
	Chains	:	A, C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET32A
	Expression System Strain	:	BL21 (DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	CORE DOMAIN
	Gene	:	NEF
	Organism Common	:	SIV-CPZ
	Organism Scientific	:	SIMIAN IMMUNODEFICIENCY VIRUS
	Organism Taxid	:	388909

Molecule 2 - T-CELL SURFACE GLYCOPROTEIN CD3 ZETA CHAIN
	Chains	:	B, D
	Engineered	:	YES
	Fragment	:	ITAM 1 POLYPEPTIDE (A63-R80)
	Other Details	:	THIS SEQUENCE OCCURS NATURALLY IN HUMANS.
	Synonym	:	T-CELL RECEPTOR T3 ZETA CHAIN
	Synthetic	:	YES

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A	B	C	D
Biological Unit 2 (1x)	:	A	B
Biological Unit 3 (1x)	:			C	D

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 3IK5)

(no "Site" information available for 3IK5)

(no "SS Bond" information available for 3IK5)

Asymmetric Unit

No.	Residues
1	Gly A:162	-	Pro A:163
2	Gly C:162	-	Pro C:163

(no "SAP(SNP)/Variant" information available for 3IK5)

(no "PROSITE Motif" information available for 3IK5)

Asymmetric Unit (2, 4)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1b	ENST00000362089	1b	ENSE00001897306	chr1:167487775-167487645	131	CD3Z_HUMAN	1-20	20	0	-	-
1.2a	ENST00000362089	2a	ENSE00001164461	chr1:167410004-167409901	104	CD3Z_HUMAN	20-54	35	0	-	-
1.3c	ENST00000362089	3c	ENSE00000958523	chr1:167408637-167408581	57	CD3Z_HUMAN	55-73	19	2	B:63-73 D:63-73	11 11
1.4	ENST00000362089	4	ENSE00000958524	chr1:167407887-167407807	81	CD3Z_HUMAN	74-100	27	2	B:74-78 D:74-77	5 4
1.5a	ENST00000362089	5a	ENSE00001067430	chr1:167404671-167404636	36	CD3Z_HUMAN	101-112	12	0	-	-
1.5d	ENST00000362089	5d	ENSE00000958526	chr1:167403313-167403257	57	CD3Z_HUMAN	113-131	19	0	-	-
1.6	ENST00000362089	6	ENSE00000958527	chr1:167402296-167402261	36	CD3Z_HUMAN	132-143	12	0	-	-
1.7d	ENST00000362089	7d	ENSE00001924110	chr1:167400983-167399877	1107	CD3Z_HUMAN	144-164	21	0	-	-

Asymmetric Unit

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	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
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Chain A from PDB  Type:PROTEIN  Length:119
 aligned with NEF_SIVMA | P31818 from UniProtKB/Swiss-Prot  Length:263

    Alignment length:135
                                   109       119       129       139       149       159       169       179       189       199       209       219       229     
            NEF_SIVMA   100 DTVRPKVPLRTMSYKLAIDMSHFIKEKGGLEGIYYSARRHRILDIYLEKEEGIIPDWQDYTSGPGIRYPKTFGWLWKLVPVNVSDEAQEDEEHYLMHPAQTSQWDDPWGEVPAWKFDPTLAYTYEAYVRYPEEFG 234
               SCOP domains d3ik5a_ A: automated matches                                                                                                            SCOP domains
               CATH domains 3ik5A00 A:100-234 Nef Regulatory Factor                                                                                                 CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............hhhhhhhhhhhhhhh........hhhhhhhhhhhhhhh.........................eeeee.----------------..............eeeee.hhhhh.hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ik5 A 100 VSVRPKVPLRTMSYKLAIDMSHFIKEKGGLEGIYYSARRHRILDIYLEKEEGIIPDWQDYTSGPGIRYPKTFGWLWKLVPV----------------PAQTSQWDDPWGEVLAWKFDPTLAYTYEAYVRYPEEFG 234
                                   109       119       129       139       149       159       169       179|        -       199       209       219       229     
                                                                                                          180              197

Chain A from PDB  Type:PROTEIN  Length:119
 aligned with Q5QGG3_SIV | Q5QGG3 from UniProtKB/TrEMBL  Length:263

    Alignment length:135
                                   109       119       129       139       149       159       169       179       189       199       209       219       229     
           Q5QGG3_SIV   100 VSVRPKVPLRTMSYKLAIDMSHFIKEKGGLEGIYYSARRHRILDIYLEKEEGIIPDWQDYTSGPGIRYPKTFGWLWKLVPVNVSDEAQEDEEHYLMHPAQTSQWDDPWGEVLAWKFDPTLAYTYEAYVRYPEEFG 234
               SCOP domains d3ik5a_ A: automated matches                                                                                                            SCOP domains
               CATH domains 3ik5A00 A:100-234 Nef Regulatory Factor                                                                                                 CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............hhhhhhhhhhhhhhh........hhhhhhhhhhhhhhh.........................eeeee.----------------..............eeeee.hhhhh.hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ik5 A 100 VSVRPKVPLRTMSYKLAIDMSHFIKEKGGLEGIYYSARRHRILDIYLEKEEGIIPDWQDYTSGPGIRYPKTFGWLWKLVPV----------------PAQTSQWDDPWGEVLAWKFDPTLAYTYEAYVRYPEEFG 234
                                   109       119       129       139       149       159       169       179|        -       199       209       219       229     
                                                                                                          180              197

Chain B from PDB  Type:PROTEIN  Length:16
 aligned with CD3Z_HUMAN | P20963 from UniProtKB/Swiss-Prot  Length:164

    Alignment length:16
                                    72      
           CD3Z_HUMAN    63 AYQQGQNQLYNELNLG  78
               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 1 Exon 1.3c  1.4   Transcript 1
                 3ik5 B  63 AYQQGQNQLYNELNLG  78
                                    72

Chain C from PDB  Type:PROTEIN  Length:117
 aligned with NEF_SIVMA | P31818 from UniProtKB/Swiss-Prot  Length:263

    Alignment length:135
                                   109       119       129       139       149       159       169       179       189       199       209       219       229     
            NEF_SIVMA   100 DTVRPKVPLRTMSYKLAIDMSHFIKEKGGLEGIYYSARRHRILDIYLEKEEGIIPDWQDYTSGPGIRYPKTFGWLWKLVPVNVSDEAQEDEEHYLMHPAQTSQWDDPWGEVPAWKFDPTLAYTYEAYVRYPEEFG 234
               SCOP domains d3ik5c_ C: automated matches                                                                                                            SCOP domains
               CATH domains 3ik5C00 C:100-234 Nef Regulatory Factor                                                                                                 CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............hhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhh.........................eeeee..------------------...........eeeee.hhhhh.hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ik5 C 100 VSVRPKVPLRTMSYKLAIDMSHFIKEKGGLEGIYYSARRHRILDIYLEKEEGIIPDWQDYTSGPGIRYPKTFGWLWKLVPVN------------------TSQWDDPWGEVLAWKFDPTLAYTYEAYVRYPEEFG 234
                                   109       119       129       139       149       159       169       179 |       -         -|      209       219       229     
                                                                                                           181                200

Chain C from PDB  Type:PROTEIN  Length:117
 aligned with Q5QGG3_SIV | Q5QGG3 from UniProtKB/TrEMBL  Length:263

    Alignment length:135
                                   109       119       129       139       149       159       169       179       189       199       209       219       229     
           Q5QGG3_SIV   100 VSVRPKVPLRTMSYKLAIDMSHFIKEKGGLEGIYYSARRHRILDIYLEKEEGIIPDWQDYTSGPGIRYPKTFGWLWKLVPVNVSDEAQEDEEHYLMHPAQTSQWDDPWGEVLAWKFDPTLAYTYEAYVRYPEEFG 234
               SCOP domains d3ik5c_ C: automated matches                                                                                                            SCOP domains
               CATH domains 3ik5C00 C:100-234 Nef Regulatory Factor                                                                                                 CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............hhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhh.........................eeeee..------------------...........eeeee.hhhhh.hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ik5 C 100 VSVRPKVPLRTMSYKLAIDMSHFIKEKGGLEGIYYSARRHRILDIYLEKEEGIIPDWQDYTSGPGIRYPKTFGWLWKLVPVN------------------TSQWDDPWGEVLAWKFDPTLAYTYEAYVRYPEEFG 234
                                   109       119       129       139       149       159       169       179 |       -         -|      209       219       229     
                                                                                                           181                200

Chain D from PDB  Type:PROTEIN  Length:15
 aligned with CD3Z_HUMAN | P20963 from UniProtKB/Swiss-Prot  Length:164

    Alignment length:15
                                    72     
           CD3Z_HUMAN    63 AYQQGQNQLYNELNL  77
               SCOP domains --------------- SCOP domains
               CATH domains --------------- CATH domains
               Pfam domains --------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------- SAPs(SNPs)
                    PROSITE --------------- PROSITE
               Transcript 1 Exon 1.3c  1.4  Transcript 1
                 3ik5 D  63 AYQQGQNQLYNELNL  77
                                    72

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: Alpha and beta proteins (a+b) (23004)

Fold: Regulatory factor Nef (10)

Superfamily: Regulatory factor Nef (10)

Family: automated matches (2)

Protein domain: automated matches (2)

Simian immunodeficiency virus [TaxId: 388909] (1)

1a	d3ik5a_	A:
1b	d3ik5c_	C:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Nef Regulatory Factor (6)

Homologous Superfamily: Nef Regulatory Factor (6)

Siv-cpz (Simian immunodeficiency virus) (1)

1a	3ik5C00	C:100-234
1b	3ik5A00	A:100-234

(no "Pfam Domain" information available for 3IK5)

Asymmetric Unit(hide GO term definitions)

Chain A,C (NEF_SIVMA | P31818)

molecular function
	GO:0005525	GTP binding	Interacting selectively and non-covalently with GTP, guanosine triphosphate.
biological process
	GO:0030683	evasion or tolerance by virus of host immune response	Any process, either active or passive, by which a virus avoids the effects of the host organism's immune response. The host is defined as the larger of the organisms involved in a symbiotic interaction.
	GO:0009405	pathogenesis	The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
	GO:0016032	viral process	A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
cellular component
	GO:0033644	host cell membrane	Double layer of lipid molecules as it encloses host cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins. The host is defined as the larger of the organisms involved in a symbiotic interaction.
	GO:0020002	host cell plasma membrane	The plasma membrane surrounding a host cell.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

Chain A,C (Q5QGG3_SIV | Q5QGG3)

molecular function
	GO:0005525	GTP binding	Interacting selectively and non-covalently with GTP, guanosine triphosphate.
biological process
	GO:0030683	evasion or tolerance by virus of host immune response	Any process, either active or passive, by which a virus avoids the effects of the host organism's immune response. The host is defined as the larger of the organisms involved in a symbiotic interaction.
	GO:0009405	pathogenesis	The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
	GO:0016032	viral process	A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
cellular component
	GO:0033644	host cell membrane	Double layer of lipid molecules as it encloses host cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins. The host is defined as the larger of the organisms involved in a symbiotic interaction.
	GO:0020002	host cell plasma membrane	The plasma membrane surrounding a host cell.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

Chain B,D (CD3Z_HUMAN | P20963)

molecular function
	GO:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0042803	protein homodimerization activity	Interacting selectively and non-covalently with an identical protein to form a homodimer.
	GO:0004888	transmembrane signaling receptor activity	Combining with an extracellular or intracellular signal and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity or state as part of signal transduction.
biological process
	GO:0038096	Fc-gamma receptor signaling pathway involved in phagocytosis	An Fc-gamma receptor signaling pathway that contributes to the endocytic engulfment of external particulate material by phagocytes.
	GO:0031295	T cell costimulation	The process of providing, via surface-bound receptor-ligand pairs, a second, antigen-independent, signal in addition to that provided by the T cell receptor to augment T cell activation.
	GO:0050852	T cell receptor signaling pathway	A series of molecular signals initiated by the cross-linking of an antigen receptor on a T cell.
	GO:0007166	cell surface receptor signaling pathway	A series of molecular signals initiated by activation of a receptor on the surface of a cell. The pathway begins with binding of an extracellular ligand to a cell surface receptor, or for receptors that signal in the absence of a ligand, by ligand-withdrawal or the activity of a constitutively active receptor. The pathway ends with regulation of a downstream cellular process, e.g. transcription.
	GO:0050690	regulation of defense response to virus by virus	Any viral process that modulates the frequency, rate, or extent of the antiviral response of the host cell or organism.
	GO:0050776	regulation of immune response	Any process that modulates the frequency, rate or extent of the immune response, the immunological reaction of an organism to an immunogenic stimulus.
	GO:0016032	viral process	A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
cellular component
	GO:0042101	T cell receptor complex	A protein complex that contains a disulfide-linked heterodimer of T cell receptor (TCR) chains, which are members of the immunoglobulin superfamily, and mediates antigen recognition, ultimately resulting in T cell activation. The TCR heterodimer is associated with the CD3 complex, which consists of the nonpolymorphic polypeptides gamma, delta, epsilon, zeta, and, in some cases, eta (an RNA splice variant of zeta) or Fc epsilon chains.
	GO:0042105	alpha-beta T cell receptor complex	A T cell receptor complex in which the TCR heterodimer comprises alpha and beta chains, associated with the CD3 complex; recognizes a complex consisting of an antigen-derived peptide bound to a class I or class II MHC protein.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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	Cis Peptide Bonds
		Gly A:162 - Pro A:163	[ RasMol ]
		Gly C:162 - Pro C:163	[ RasMol ]

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(no "Related Entries Specified in the PDB File" available for 3IK5)

Description

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Ligands, Modified Residues, Ions (0, 0)

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Cis Peptide Bonds (2, 2)

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Exons (2, 4)

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