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Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   STRUCTURE OF HUMAN MR1-5-OP-RU IN COMPLEX WITH HUMAN MAIT TRBV20 TCR

Authors :   R. W. Birkinshaw, J. Rossjohn

Date :   12 May 14 (Deposition) - 02 Jul 14 (Release) - 01 Oct 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.30

Chains :   Asym./Biol. Unit : A,B,C,D

Keywords :   Mr1, Tcr, Immune Complex, 5-Op-Ru, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. B. Eckle, R. W. Birkinshaw, L. Kostenko, A. J. Corbett, H. E. Mcwilliam, R. Reantragoon, Z. Chen, N. A. Gherardin, T. Beddoe, L. Liu, O. Patel, B. Meehan, D. P. Fairlie, J. A. Villadangos, D. I. Godfrey, L. Kjer-Nielsen, J. Mccluskey, J. Rossjohn
A Molecular Basis Underpinning The T Cell Receptor Heterogeneity Of Mucosal-Associated Invariant T Cells.
J. Exp. Med. V. 211 1585 2014
PubMed-ID: 25049336 | Reference-DOI: 10.1084/JEM.20140484

Molecule 1 - MAJOR HISTOCOMPATIBILITY COMPLEX CLASS I-RELATED GENE PROTEIN
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	469008
	Fragment	:	UNP RESIDUES 23-292
	Gene	:	MR1
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	MHC CLASS I-RELATED GENE PROTEIN,CLASS I HISTOCOMPATIBILITY ANTIGEN-LIKE PROTEIN

Molecule 2 - BETA-2-MICROGLOBULIN
	Chains	:	B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	469008
	Gene	:	B2M, CDABP0092, HDCMA22P
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

Molecule 3 - TCR-ALPHA
	Chains	:	C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	469008
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

Molecule 4 - TCR-BETA
	Chains	:	D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	469008
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 2)

No.	Name	Count	Type	Full Name
1	2LJ	1	Ligand/Ion	1-DEOXY-1-({2,6-DIOXO-5-[(E)-(2-OXOPROPYLIDENE)AMINO]-1,2,3,6-TETRAHYDROPYRIMIDIN-4-YL}AMINO)-D-RIBITOL
2	NA	1	Ligand/Ion	SODIUM ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TYR A:7 , ARG A:9 , SER A:24 , LYS A:43 , HIS A:58 , LEU A:66 , TRP A:69 , ARG A:94 , ILE A:96 , TYR A:152 , GLN A:153 , TRP A:156 , TYR C:95 , ASP D:101	binding site for residue 2LJ A 301
2	AC2	SOFTWARE	GLN C:2 , THR C:26 , SER C:27 , GLY C:28 , ASP C:92 , SER C:93	binding site for residue NA C 301

Asymmetric/Biological Unit

No.	Residues
1	A:98	-	A:161
2	A:200	-	A:256
3	B:25	-	B:80
4	C:22	-	C:88
5	C:132	-	C:182
6	C:157	-	D:173
7	D:23	-	D:94
8	D:147	-	D:212

Asymmetric/Biological Unit

No.	Residues
1	Tyr A:206	-	Pro A:207
2	His B:31	-	Pro B:32
3	His D:7	-	Pro D:8
4	Pro D:40	-	Lys D:41
5	Gly D:110	-	Thr D:111
6	Tyr D:153	-	Pro D:154

(no "SAP(SNP)/Variant" information available for 4PJ8)

(no "PROSITE Motif" information available for 4PJ8)

(no "Exon" information available for 4PJ8)

Asymmetric/Biological 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:260
                                                                                                                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeee.......eeeeeee..eeeeeee......ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeeeeeee.....eeeeeeeee..eeeeeee....eeee.hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeeee.......eeeeeeeee.....eeeeee..ee...eeeeeee.....eeeeeee....eeeeeee..eeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4pj8 A   1 RTHSLRYFRLGVSDPIVPEFISVGYVDSHPITTYDSVTRQKEPRAPWMAENLAPDHWERYTQLLRGWQQMFKVELKRLQRHYNHSGSHTYQRMIGCELLEDGSTTGFLQYAYDGQDFLIFNKDTLSWLAVDNVAHTIKQAWEANQHELLYQKNWLEEECIAWLKRFLEYGKDTLQRTEPPLVRVNRKETFPGVTALFCKAHGFYPPEIYMTWMKNGEEIEIDYGDILPSGDGTYQAWASIESNLYSCHVEHSGVHMVLQV 269
                                    10     || 22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       224       234       244||     259       269
                                          16|                                                                                                                                                                                                       221|                  245|                  
                                           19                                                                                                                                                                                                        224                   251

Chain B from PDB  Type:PROTEIN  Length:97
                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeee.........eeeeeeeeee.....eeeeee.............ee.....eeeeeeeee.......eeeeee.......eeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------- Transcript
                 4pj8 B   1 IQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDWSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDR  97
                                    10        20        30        40        50        60        70        80        90

Chain C from PDB  Type:PROTEIN  Length:197
                                                                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee...eeeee....eeeeeeee...eeeeeeeee......eeeeee...eeeee..eeeeee....eeeeee...hhhhh.eeeeeeee....eee...eeeeee........eeeeeee......eeeeeeee.............eee...eeee......eeeeeeeee....................... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4pj8 C   2 QNIDQPTEMTATEGAIVQINCTYQTSGFNGLFWYQQHAGEAPTFLSYNVLDGLEEKGRFSSFLSRSKGYSYLLLKELQMKDSASYLCAFMDSNYQLIWGAGTKLIIKPDIQNPDPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKSDFACANAFNNSIIPEDTFFP 198
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191

Chain D from PDB  Type:PROTEIN  Length:244
                                                                                                                                                                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee....eeeee....eeeeeee......eeeeee.......eeeeeee.....ee...........ee....eeeeee...hhhhheeeeeeee.......eee....eeeee.hhhhh...eeeeee.hhhhhhhhheeeeeeeeeee....eeeeeee..eee...eee....ee.........eeeeeeeeeehhhhhh...eeeeeeee..................eeeeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4pj8 D   2 AVVSQHPSWVISKSGTSVKIECRSLDFQATTMFWYRQFPKQSLMLMATSNEGSKATYEQGVEKDKFLINHASLTLSTLTVTSAHPEDSSFYICSARTSGDFGEQFFGPGTRLTVLEDLKNVFPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQPALNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGRA 245
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241

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 4PJ8)

(no "CATH Domain" information available for 4PJ8)

(no "Pfam Domain" information available for 4PJ8)

Asymmetric/Biological Unit(hide GO term definitions)

Asymmetric/Biological Unit
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	Ligands, Modified Residues, Ions
		2LJ	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		NA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Gly D:110 - Thr D:111	[ RasMol ]
		His B:31 - Pro B:32	[ RasMol ]
		His D:7 - Pro D:8	[ RasMol ]
		Pro D:40 - Lys D:41	[ RasMol ]
		Tyr A:206 - Pro A:207	[ RasMol ]
		Tyr D:153 - Pro D:154	[ RasMol ]

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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 2)

Sites (2, 2)

SS Bonds (8, 8)

Cis Peptide Bonds (6, 6)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (64, 74)

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