3RWH - JenaLib

Asymmetric Unit (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   RHESUS MACAQUE MHC CLASS I MOLECULE MAMU-B*17-MF8

Authors :   Y. Wu, F. Gao, J. Liu, J. X. Qi, D. A. Price, G. F. Gao

Date :   09 May 11 (Deposition) - 21 Mar 12 (Release) - 21 Mar 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.60

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

Keywords :   Antigenic Peptides, T Lymphocytes, Immune Response, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. Wu, F. Gao, J. Liu, J. X. Qi, E. Gostick, D. A. Price, G. F. Gao
Structural Basis Of Diverse Peptide Accommodation By The Rhesus Macaque Mhc Class I Molecule Mamu-B*17: Insights Int Immune Protection From Simian Immunodeficiency Virus
J. Immunol. V. 187 6382 2011
PubMed-ID: 22084443 | Reference-DOI: 10.4049/JIMMUNOL.1101726

Molecule 1 - MAJOR HISTOCOMPATIBILITY COMPLEX CLASS I
	Chains	:	A, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	RESIDUES 24-297
	Gene	:	MHCI-B
	Organism Common	:	RHESUS MACAQUE
	Organism Scientific	:	MACACA MULATTA
	Organism Taxid	:	9544

Molecule 2 - BETA-2-MICROGLOBULIN
	Chains	:	B, E
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	B2M
	Organism Common	:	RHESUS MACAQUE
	Organism Scientific	:	MACACA MULATTA
	Organism Taxid	:	9544

Molecule 3 - POL MF8 PEPTIDE FROM POL PROTEIN
	Chains	:	C, F
	Engineered	:	YES
	Organism Common	:	SIV-CPZ
	Organism Scientific	:	SIMIAN IMMUNODEFICIENCY VIRUS
	Organism Taxid	:	11723
	Other Details	:	SYNTHTIC PEPTIDE
	Synthetic	:	YES

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

Summary Information (see also Sequences/Alignments below)

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

(no "Site" information available for 3RWH)

Asymmetric Unit

No.	Residues
1	A:101	-	A:164
2	A:203	-	A:259
3	B:25	-	B:80
4	D:101	-	D:164
5	D:203	-	D:259
6	E:25	-	E:80

Asymmetric Unit

No.	Residues
1	Tyr A:209	-	Pro A:210
2	His B:31	-	Pro B:32
3	Tyr D:209	-	Pro D:210
4	His E:31	-	Pro E:32

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

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	IG_MHC	PS00290	Immunoglobulins and major histocompatibility complex proteins signature.	B2MG_MACMU	98-104	2	B:78-84 E:78-84

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	IG_MHC	PS00290	Immunoglobulins and major histocompatibility complex proteins signature.	B2MG_MACMU	98-104	1	B:78-84 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	IG_MHC	PS00290	Immunoglobulins and major histocompatibility complex proteins signature.	B2MG_MACMU	98-104	1	- E:78-84

(no "Exon" information available for 3RWH)

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:276
 aligned with Q9GJ77_MACMU | Q9GJ77 from UniProtKB/TrEMBL  Length:361

    Alignment length:276
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293      
         Q9GJ77_MACMU    24 GSHSMKYFYTSVSRPGRGEPRFISVGYVDDTQFVRFDSDAESPREEPRAPWVEQEGPEYWEEATRRAKEAAQTHRENLRTALRYYNQSEAGSHTIQKMYGCDLGPDGRLLRGYHQSAYDGKDYIALNGDLRSWTAADMAAQNTQRKWEGNRYAERFRAYLEGECLEWLRRYLENGKETLQRADPPKTHVTHHPVSDHEATLRCWALGFYPAEITLTWQRDGEEQTQDTEFVETRPGGDGTFQKWGAVVVPSGEEQRYTCHVQHEGLPEPLTLRWEP 299
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeeeeee........eeeeeeee..eeeeeee........ee.hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........eeeeeeeeee.....eeeeeeeeee..eeeeee......eee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeeeee....eeeeeeeeeee.....eeeeee..eee...eee...ee.....eeeeeeeeee..hhh.eeeeee.......eee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3rwh A   1 GSHSMKYFYTSVSRPGRGEPRFISVGYVDDTQFVRFDSDAESPREEPRAPWVEQEGPEYWEEATRRAKEAAQTHRENLRTALRYYNQSEAGSHTIQKMYGCDLGPDGRLLRGYHQSAYDGKDYIALNGDLRSWTAADMAAQNTQRKWEGNRYAERFRAYLEGECLEWLRRYLENGKETLQRADPPKTHVTHHPVSDHEATLRCWALGFYPAEITLTWQRDGEEQTQDTEFVETRPGGDGTFQKWGAVVVPSGEEQRYTCHVQHEGLPEPLTLRWEP 276
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270

Chain B from PDB  Type:PROTEIN  Length:98
 aligned with B2MG_MACMU | Q6V7J5 from UniProtKB/Swiss-Prot  Length:119

    Alignment length:98
                                    31        41        51        61        71        81        91       101       111        
           B2MG_MACMU    22 QRTPKIQVYSRHPPENGKPNFLNCYVSGFHPSDIEVDLLKNGEKMGKVEHSDLSFSKDWSFYLLYYTEFTPNEKDEYACRVNHVTLSGPRTVKWDRDM 119
               SCOP domains -------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee.........eeeeeeeeee....eeeeeee..ee....ee...ee.....eeeeeeeee.......eeeeeee......eeee..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------IG_MHC --------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------- Transcript
                 3rwh B   2 QRTPKIQVYSRHPPENGKPNFLNCYVSGFHPSDIEVDLLKNGEKMGKVEHSDLSFSKDWSFYLLYYTEFTPNEKDEYACRVNHVTLSGPRTVKWDRDM  99
                                    11        21        31        41        51        61        71        81        91

Chain C from PDB  Type:PROTEIN  Length:8
 aligned with Q5QGH9_SIV | Q5QGH9 from UniProtKB/TrEMBL  Length:1060

    Alignment length:8
           Q5QGH9_SIV   372 MRHVLEPF 379
               SCOP domains -------- SCOP domains
               CATH domains -------- CATH domains
               Pfam domains -------- Pfam domains
         Sec.struct. author ........ Sec.struct. author
                 SAPs(SNPs) -------- SAPs(SNPs)
                    PROSITE -------- PROSITE
                 Transcript -------- Transcript
                 3rwh C   1 MRHVLEPF   8

Chain D from PDB  Type:PROTEIN  Length:276
 aligned with Q9GJ77_MACMU | Q9GJ77 from UniProtKB/TrEMBL  Length:361

    Alignment length:276
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293      
         Q9GJ77_MACMU    24 GSHSMKYFYTSVSRPGRGEPRFISVGYVDDTQFVRFDSDAESPREEPRAPWVEQEGPEYWEEATRRAKEAAQTHRENLRTALRYYNQSEAGSHTIQKMYGCDLGPDGRLLRGYHQSAYDGKDYIALNGDLRSWTAADMAAQNTQRKWEGNRYAERFRAYLEGECLEWLRRYLENGKETLQRADPPKTHVTHHPVSDHEATLRCWALGFYPAEITLTWQRDGEEQTQDTEFVETRPGGDGTFQKWGAVVVPSGEEQRYTCHVQHEGLPEPLTLRWEP 299
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeeeee........eeeeeeee..eeeeeee........ee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........eeeeeeeeee.....eeeeeeeeee..eeeeee......eee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........eeeeeeee....eeeeeeeeeee.....eeeeee..eee...eee...ee.....eeeeeeeeee..hhh.eeeeee.......eee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3rwh D   1 GSHSMKYFYTSVSRPGRGEPRFISVGYVDDTQFVRFDSDAESPREEPRAPWVEQEGPEYWEEATRRAKEAAQTHRENLRTALRYYNQSEAGSHTIQKMYGCDLGPDGRLLRGYHQSAYDGKDYIALNGDLRSWTAADMAAQNTQRKWEGNRYAERFRAYLEGECLEWLRRYLENGKETLQRADPPKTHVTHHPVSDHEATLRCWALGFYPAEITLTWQRDGEEQTQDTEFVETRPGGDGTFQKWGAVVVPSGEEQRYTCHVQHEGLPEPLTLRWEP 276
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270

Chain E from PDB  Type:PROTEIN  Length:98
 aligned with B2MG_MACMU | Q6V7J5 from UniProtKB/Swiss-Prot  Length:119

    Alignment length:98
                                    31        41        51        61        71        81        91       101       111        
           B2MG_MACMU    22 QRTPKIQVYSRHPPENGKPNFLNCYVSGFHPSDIEVDLLKNGEKMGKVEHSDLSFSKDWSFYLLYYTEFTPNEKDEYACRVNHVTLSGPRTVKWDRDM 119
               SCOP domains -------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee.........eeeeeeeeee....eeeeeee..ee....ee...ee.....eeeeeeeee.......eeeeeee......eeee..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------IG_MHC --------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------- Transcript
                 3rwh E   2 QRTPKIQVYSRHPPENGKPNFLNCYVSGFHPSDIEVDLLKNGEKMGKVEHSDLSFSKDWSFYLLYYTEFTPNEKDEYACRVNHVTLSGPRTVKWDRDM  99
                                    11        21        31        41        51        61        71        81        91

Chain F from PDB  Type:PROTEIN  Length:8
 aligned with Q5QGH9_SIV | Q5QGH9 from UniProtKB/TrEMBL  Length:1060

    Alignment length:8
           Q5QGH9_SIV   372 MRHVLEPF 379
               SCOP domains -------- SCOP domains
               CATH domains -------- CATH domains
               Pfam domains -------- Pfam domains
         Sec.struct. author ........ Sec.struct. author
                 SAPs(SNPs) -------- SAPs(SNPs)
                    PROSITE -------- PROSITE
                 Transcript -------- Transcript
                 3rwh F   1 MRHVLEPF   8

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 3RWH)

(no "CATH Domain" information available for 3RWH)

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

Asymmetric Unit(hide GO term definitions)

Chain A,D (Q9GJ77_MACMU | Q9GJ77)

molecular function
	GO:0042605	peptide antigen binding	Interacting selectively and non-covalently with an antigen peptide.
biological process
	GO:0019882	antigen processing and presentation	The process in which an antigen-presenting cell expresses antigen (peptide or lipid) on its cell surface in association with an MHC protein complex.
	GO:0002474	antigen processing and presentation of peptide antigen via MHC class I	The process in which an antigen-presenting cell expresses a peptide antigen on its cell surface in association with an MHC class I protein complex. Class I here refers to classical class I molecules.
	GO:0006955	immune response	Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat.
	GO:0002376	immune system process	Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.
cellular component
	GO:0042612	MHC class I protein complex	A transmembrane protein complex composed of a MHC class I alpha chain and an invariant beta2-microglobin chain, and with or without a bound peptide antigen. Class I here refers to classical class I molecules.
	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.

Chain B,E (B2MG_MACMU | Q6V7J5)

biological process
	GO:0002474	antigen processing and presentation of peptide antigen via MHC class I	The process in which an antigen-presenting cell expresses a peptide antigen on its cell surface in association with an MHC class I protein complex. Class I here refers to classical class I molecules.
	GO:0006955	immune response	Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat.
	GO:0002376	immune system process	Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.
cellular component
	GO:0042612	MHC class I protein complex	A transmembrane protein complex composed of a MHC class I alpha chain and an invariant beta2-microglobin chain, and with or without a bound peptide antigen. Class I here refers to classical class I molecules.
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

Chain C,F (Q5QGH9_SIV | Q5QGH9)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0004523	RNA-DNA hybrid ribonuclease activity	Catalysis of the endonucleolytic cleavage of RNA in RNA-DNA hybrids to 5'-phosphomonoesters.
	GO:0003964	RNA-directed DNA polymerase activity	Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1). Catalyzes RNA-template-directed extension of the 3'- end of a DNA strand by one deoxynucleotide at a time.
	GO:0004190	aspartic-type endopeptidase activity	Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which a water molecule bound by the side chains of aspartic residues at the active center acts as a nucleophile.
	GO:0003824	catalytic activity	Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
	GO:0004519	endonuclease activity	Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0004518	nuclease activity	Catalysis of the hydrolysis of ester linkages within nucleic acids.
	GO:0003676	nucleic acid binding	Interacting selectively and non-covalently with any nucleic acid.
	GO:0016779	nucleotidyltransferase activity	Catalysis of the transfer of a nucleotidyl group to a reactant.
	GO:0008233	peptidase activity	Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
	GO:0016740	transferase activity	Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0015074	DNA integration	The process in which a segment of DNA is incorporated into another, usually larger, DNA molecule such as a chromosome.
	GO:0006310	DNA recombination	Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Intrachromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction.
	GO:0090502	RNA phosphodiester bond hydrolysis, endonucleolytic	The chemical reactions and pathways involving the hydrolysis of internal 3',5'-phosphodiester bonds in one or two strands of ribonucleotides.
	GO:0006278	RNA-dependent DNA biosynthetic process	A DNA biosynthetic process that uses RNA as a template for RNA-dependent DNA polymerases (e.g. reverse transcriptase) that synthesize the new strand.
	GO:0075713	establishment of integrated proviral latency	A process by which the virus integrates into the host genome and establishes as a stable provirus or prophage.
	GO:0008152	metabolic process	The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
	GO:0090305	nucleic acid phosphodiester bond hydrolysis	The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
	GO:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
	GO:0046718	viral entry into host cell	The process that occurs after viral attachment by which a virus, or viral nucleic acid, breaches the plasma membrane or cell envelope and enters the host cell. The process ends when the viral nucleic acid is released into the host cell cytoplasm.

Asymmetric Unit
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	Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 3rwh)

	Sites
(no "Sites" information available for 3rwh)

	Cis Peptide Bonds
		His B:31 - Pro B:32	[ RasMol ]
		His E:31 - Pro E:32	[ RasMol ]
		Tyr A:209 - Pro A:210	[ RasMol ]
		Tyr D:209 - Pro D:210	[ RasMol ]

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	3rwh
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	B2MG_MACMU \| Q6V7J5
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	Q5QGH9_SIV \| Q5QGH9
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	Q9GJ77_MACMU \| Q9GJ77
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	B2MG_MACMU \| Q6V7J5
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	Q5QGH9_SIV \| Q5QGH9
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	Q9GJ77_MACMU \| Q9GJ77
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UniProtKB/Swiss-Prot
	B2MG_MACMU \| Q6V7J5	:	3jtt 3rwc 3rwd 3rwe 3rwf 3rwg 3rwi 4zfz
UniProtKB/TrEMBL
	Q5QGH9_SIV \| Q5QGH9	:	2sam 3rwe
	Q9GJ77_MACMU \| Q9GJ77	:	3rwc 3rwd 3rwe 3rwf 3rwg 3rwi 3rwj

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (6, 6)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (32, 36)

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