4L9L - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF A HUMAN VALPHA7.2/VBETA13.2 MAIT TCR IN COMPLEX WITH BOVINE MR1

Authors :   J. Lopez-Sagaseta, E. J. Adams

Date :   18 Jun 13 (Deposition) - 16 Oct 13 (Release) - 20 Nov 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.40

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

Keywords :   Immunoglobulin Domain, Mhc-Class I-Like, Antigen Presentation, Antigen Recognition, Vitamin Metabolites, Cell Membrane, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Lopez-Sagaseta, C. L. Dulberger, A. Mcfedries, M. Cushman, A. Saghatelian, E. J. Adams
Mait Recognition Of A Stimulatory Bacterial Antigen Bound T Mr1.
J. Immunol. V. 191 5268 2013
PubMed-ID: 24108697 | Reference-DOI: 10.4049/JIMMUNOL.1301958

Molecule 1 - BETA-2-MICROGLOBULIN, MHC CLASS I-RELATED PROTEIN
	Chains	:	C
	Engineered	:	YES
	Expression System	:	TRICHOPLUSIA NI
	Expression System Plasmid	:	PACGP67A
	Expression System Taxid	:	7111
	Expression System Vector Type	:	BACULOVIRUS
	Gene	:	MR1, BT.63045
	Organism Common	:	BOVINE,COW,DOMESTIC CATTLE,DOMESTIC COW
	Organism Scientific	:	BOS TAURUS
	Organism Taxid	:	9913
	Other Details	:	FUSION PROTEIN

Molecule 2 - HUMAN MAIT TCR ALPHA CHAIN
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28A
	Expression System Strain	:	ROSETTA (DE3)PLYSS
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

Molecule 3 - HUMAN MAIT TCR BETA CHAIN
	Chains	:	B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28A
	Expression System Strain	:	ROSETTA (DE3)PLYSS
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 3)

No.	Name	Count	Type	Full Name
1	KFP	1	Mod. Amino Acid	N~6~-[(2-AMINO-4-OXO-3,4-DIHYDROPTERIDIN-6-YL)METHYL]-D-LYSINE
2	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 3)

No.	Name	Count	Type	Full Name
1	KFP	1	Mod. Amino Acid	N~6~-[(2-AMINO-4-OXO-3,4-DIHYDROPTERIDIN-6-YL)METHYL]-D-LYSINE
2	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	KFP	-1	Mod. Amino Acid	N~6~-[(2-AMINO-4-OXO-3,4-DIHYDROPTERIDIN-6-YL)METHYL]-D-LYSINE
2	SO4	-1	Ligand/Ion	SULFATE ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:59 , LYS A:81	BINDING SITE FOR RESIDUE SO4 A 301
2	AC2	SOFTWARE	GLY B:173 , HIS B:217 , ARG B:219 , LYS C:296 , ARG C:298	BINDING SITE FOR RESIDUE SO4 B 301

Asymmetric Unit

No.	Residues
1	A:22	-	A:88
2	A:132	-	A:183
3	A:157	-	B:181
4	B:23	-	B:91
5	B:155	-	B:220
6	C:25	-	C:79
7	C:211	-	C:274
8	C:313	-	C:369

Asymmetric Unit

No.	Residues
1	His C:31	-	Pro C:32
2	Glu C:127	-	Pro C:128
3	Tyr C:319	-	Pro C:320
4	Asn C:330	-	Gly C:331
5	Gly C:375	-	Val C:376
6	Asp A:123	-	Ser A:124
7	Thr B:7	-	Pro B:8
8	Gly B:99	-	Gly B:100
9	Thr B:112	-	Val B:123
10	Tyr B:161	-	Pro B:162

(no "SAP(SNP)/Variant" information available for 4L9L)

(no "PROSITE Motif" information available for 4L9L)

(no "Exon" information available for 4L9L)

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:196
                                                                                                                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee...eeeee....eeeeeee.......eeeeee......eeeeee...eeeee..eeeeee....eeeeee...hhhhh.eeeeee............eeeeee........eeee.........eeeeee...............eeee...ee........eeeeee......................... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4l9l A   3 NIDQPTEMTATEGAIVQINCTYQTSGFNGLFWYQQHAGEAPTFLSYNVLDGLEEKGRFSSFLSRSKGYSYLLLKELQMKDSASYLCAPLDSNYQLIWGAGTKLIIKPNIQNPDPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMMDFKSNSAVAWSNKSDFACANAFNNSIIPEDTFFPSP 201
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       165       175       185       195      
                                                                                                                                                                                        161|                                    
                                                                                                                                                                                         165

Chain B from PDB  Type:PROTEIN  Length:239
                                                                                                                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee..ee.......eeeeeee.....eeeeeee......eeeeeeee..eeee..................eee...hhhhh.eeeeeee........eee...eee.........eeeee..hhhhhhhhheeeeeeeeeee....eeeeeee..eee...eee....ee.........eeeeeeeeeehhhhhh...eeeeeeee..................eeeeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4l9l B   2 AGVTQTPKFRVLKTGQSMTLLCAQDMNHEYMYWYRQDPGMGLRLIHYSVGEGTTAKGEVPDGYNVSRLKKQNFLLGLESAAPSQTSVYFCASSYPPDGGNTIYFGEGSWLTVLKNVFPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQPALNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGRA 253
                                    11        21        31        41        51        61        71        81        91       101       111|||    134       144       154       164       174       184       194       204       214       224       234       244         
                                                                                                                                        112||                                                                                                                              
                                                                                                                                         123|                                                                                                                              
                                                                                                                                          127

Chain C from PDB  Type:PROTEIN  Length:329
                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeee.....eeee..............ee.....ee..eee.eee........eee......eeeeeeeeee.........eeeeeee..eeeeee........hhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeeeeeeeee.....eeeeeeeee..eeeeeee....eeee...hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeee..eeeeeeeee.....eeeeee..ee....ee....ee.....eeeeeeee......eeeeee....eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4l9l C   1 IQRPPKIQVYSRHPPYLNCYYGFHPPQIEEQSDLSFSKDWSFYLLSHASCRVKHVTLEQPRIVKWDRRTHSLRYFRLGISEPGYGIPEFISAGYVDSHPITMYNSQLkEPRALWMEENLAPDHWERYTQLLRGWQQAFKVELKQLQHHYNHSGFHTYQRMIGCELLEDGSITGFLQYAYDGQDFLIFNKDTLSWMAMDNVADIIRRVWEANRHELQYQKNWLEEECIAWLKRFLEYGKDALQRTEPPKVRVNHKTTLYCRAYGFYPPEISINWMKNGEEIFQDTDYGGILPSGDGTYQTWVSVELQNGDIYSCHVEHGGVHMVLQGFQE 385
                                    10    ||  26|       49        59       |79        89      |116       126       136       146   ||  158       168       178       188       198       208       218       228       238       248       258       268       278       288       298   ||  314       324       334       344       354    || 366       376         
                                         15|  26|      36|                67|                96|                                 150|  |                                                                                                                                               302|                                               359|                       
                                          22   28       49                 78                114                                  153  |                                                                                                                                                309                                                362                       
                                                                                                                                     156-KFP

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 4L9L)

(no "CATH Domain" information available for 4L9L)

(no "Pfam Domain" information available for 4L9L)

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
		KFP	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		SO4	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

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

	Cis Peptide Bonds
		Asn C:330 - Gly C:331	[ RasMol ]
		Asp A:123 - Ser A:124	[ RasMol ]
		Glu C:127 - Pro C:128	[ RasMol ]
		Gly B:99 - Gly B:100	[ RasMol ]
		Gly C:375 - Val C:376	[ RasMol ]
		His C:31 - Pro C:32	[ RasMol ]
		Thr B:112 - Val B:123	[ RasMol ]
		Thr B:7 - Pro B:8	[ RasMol ]
		Tyr B:161 - Pro B:162	[ RasMol ]
		Tyr C:319 - Pro C:320	[ 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 \| Asym. Unit - sites PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 1 - sites 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
	4l9l
		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
	B2MG_BOVIN \| P01888
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt
	HMR1_BOVIN \| C1ITJ8
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt
	Q6P4G7_HUMAN \| Q6P4G7
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/TrEMBL
	TRBC1_HUMAN \| P01850
		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
	B2MG_BOVIN \| P01888
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)
	HMR1_BOVIN \| C1ITJ8
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)
	Q6P4G7_HUMAN \| Q6P4G7
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)
	TRBC1_HUMAN \| P01850
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

4iiq	SIMILAR COMPLEX STRUCTURE WITH A MAIT TCR OF DIFFERENT VBETA USAGE
4l8s	SIMILAR COMPLEX STRUCTURE WITH A MAIT TCR OF DIFFERENT VBETA USAGE
4lcc

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 3)

Sites (2, 2)

SS Bonds (8, 8)

Cis Peptide Bonds (10, 10)

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 (49, 61)

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