5L2K - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF GEM42 TCR-CD1B-GMM COMPLEX

Authors :   S. Gras, A. Shahine, J. Le Nours, J. Rossjohn

Date :   02 Aug 16 (Deposition) - 16 Nov 16 (Release) - 07 Dec 16 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.20

Chains :   Asym. Unit : A,B,D,E
Biol. Unit 1: A,B,D,E  (1x)
Biol. Unit 2: A (4x),B (4x),D (4x),E (4x)

Keywords :   Cd1B, Lipid, Tb, Mtb, Gmm, Tuberculosis, Gem T Cell, Tcr, T Cell, Gem42, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Gras, I. Van Rhijn, A. Shahine, T. Y. Cheng, M. Bhati, L. L. Tan, H. Halim, K. D. Tuttle, L. Gapin, J. Le Nours, D. B. Moody, J. Rossjohn
T Cell Receptor Recognition Of Cd1B Presenting A Mycobacterial Glycolipid.
Nat Commun V. 7 13257 2016
PubMed-ID: 27807341 | Reference-DOI: 10.1038/NCOMMS13257

Molecule 1 - T-CELL SURFACE GLYCOPROTEIN CD1B
	Chains	:	A
	Engineered	:	YES
	Expression System	:	HOMO SAPIENS
	Expression System Cell Line	:	HEK293S
	Expression System Common	:	HUMAN
	Expression System Plasmid	:	PHLSEC
	Expression System Taxid	:	9606
	Expression System Vector Type	:	PLASMID
	Gene	:	CD1B
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

Molecule 2 - BETA-2-MICROGLOBULIN
	Chains	:	B
	Engineered	:	YES
	Expression System	:	HOMO SAPIENS
	Expression System Cell Line	:	HEK293S
	Expression System Common	:	HUMAN
	Expression System Plasmid	:	PHLSEC
	Expression System Taxid	:	9606
	Expression System Vector Type	:	PLASMID
	Gene	:	B2M, CDABP0092, HDCMA22P
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

Molecule 3 - GEM42 TCR ALPHA CHAIN
	Chains	:	D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET30
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

Molecule 4 - GEM42 TCR BETA CHAIN
	Chains	:	E
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET30
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (7, 17)

No.	Name	Count	Type	Full Name
1	6UL	1	Ligand/Ion	TETRACOSYL PALMITATE
2	70E	1	Ligand/Ion	6-O-[(2R,3R)-3-HYDROXY-2-TETRADECYLDOCOSANOYL]-ALPHA-L-IDOPYRANOSE
3	CL	4	Ligand/Ion	CHLORIDE ION
4	CS	1	Ligand/Ion	CESIUM ION
5	NA	2	Ligand/Ion	SODIUM ION
6	NAG	3	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
7	SO4	5	Ligand/Ion	SULFATE ION

Biological Unit 1 (4, 10)

No.	Name	Count	Type	Full Name
1	6UL	1	Ligand/Ion	TETRACOSYL PALMITATE
2	70E	1	Ligand/Ion	6-O-[(2R,3R)-3-HYDROXY-2-TETRADECYLDOCOSANOYL]-ALPHA-L-IDOPYRANOSE
3	CL	-1	Ligand/Ion	CHLORIDE ION
4	CS	-1	Ligand/Ion	CESIUM ION
5	NA	-1	Ligand/Ion	SODIUM ION
6	NAG	3	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
7	SO4	5	Ligand/Ion	SULFATE ION

Biological Unit 2 (4, 36)

No.	Name	Count	Type	Full Name
1	6UL	4	Ligand/Ion	TETRACOSYL PALMITATE
2	70E	4	Ligand/Ion	6-O-[(2R,3R)-3-HYDROXY-2-TETRADECYLDOCOSANOYL]-ALPHA-L-IDOPYRANOSE
3	CL	-1	Ligand/Ion	CHLORIDE ION
4	CS	-1	Ligand/Ion	CESIUM ION
5	NA	-1	Ligand/Ion	SODIUM ION
6	NAG	12	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
7	SO4	16	Ligand/Ion	SULFATE ION

Asymmetric Unit (15, 15)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASN A:57 , LYS A:61 , NAG A:401 , GLN D:2	binding site for residue SO4 A 404
02	AC2	SOFTWARE	PHE A:75 , ARG A:79 , LYS E:84 , ARG E:109 , GLU E:231	binding site for residue SO4 A 405
03	AC3	SOFTWARE	ARG A:159 , NAG A:403 , PHE D:30 , ARG D:84A	binding site for residue SO4 A 406
04	AC4	SOFTWARE	SER A:139	binding site for residue CL A 407
05	AC5	SOFTWARE	THR A:8 , LEU A:104	binding site for residue CL A 409
06	AC6	SOFTWARE	GLN A:231 , ARG A:246 , THR A:248	binding site for residue NA A 410
07	AC7	SOFTWARE	ILE A:13 , TRP A:40 , TYR A:73 , ILE A:96 , ALA A:117 , PHE A:123 , LEU A:124 , PHE A:144	binding site for residue 6UL A 411
08	AC8	SOFTWARE	LYS B:43 , PHE B:72 , THR B:73	binding site for residue CL B 201
09	AC9	SOFTWARE	PRO D:8 , THR D:9 , GLU D:10	binding site for residue SO4 D 301
10	AD1	SOFTWARE	GLN E:237 , ASP E:238 , ARG E:239	binding site for residue SO4 E 301
11	AD2	SOFTWARE	HIS E:179	binding site for residue NA E 302
12	AD3	SOFTWARE	PHE A:10 , HIS A:38 , VAL A:72 , TYR A:73 , GLY A:76 , PHE A:77 , CYS A:131 , GLY A:153 , ILE A:154 , LEU A:161 , TYR A:169 , ASN D:31 , ARG D:107 , GLY D:111 , GLY D:112 , TYR E:31 , ARG E:109 , LEU E:110 , ALA E:111 , GLY E:112 , ASP E:113	binding site for residue 70E E 303
13	AD4	SOFTWARE	ASN A:20 , THR A:22 , TRP A:23	binding site for Mono-Saccharide NAG A 402 bound to ASN A 20
14	AD5	SOFTWARE	ASN A:57 , PHE A:58 , ARG A:168 , SO4 A:404 , GLN D:2 , ASN D:3	binding site for Mono-Saccharide NAG A 401 bound to ASN A 57
15	AD6	SOFTWARE	ASN A:128 , ARG A:159 , SO4 A:406 , ASP D:59 , ARG D:84A	binding site for Mono-Saccharide NAG A 403 bound to ASN A 128

Asymmetric Unit

No.	Residues
1	A:102	-	A:166
2	A:131	-	A:145
3	A:206	-	A:261
4	B:27	-	B:82
5	D:23	-	D:104
6	D:150	-	D:200
7	D:175	-	E:183
8	E:23	-	E:104
9	E:157	-	E:222

Asymmetric Unit

No.	Residues
1	Tyr A:92	-	Pro A:93
2	Tyr A:212	-	Pro A:213
3	His B:33	-	Pro B:34
4	Ala D:46	-	Gly D:47
5	Asp D:59	-	Gly D:60
6	Thr D:110	-	Gly D:111
7	Lys D:143	-	Ser D:144
8	Gln D:158	-	Thr D:159
9	Thr E:7	-	Pro E:8
10	Gly E:47	-	Met E:48
11	Asp E:74	-	Gly E:75
12	Gly E:112	-	Asp E:113
13	Tyr E:163	-	Pro E:164

(no "SAP(SNP)/Variant" information available for 5L2K)

(no "PROSITE Motif" information available for 5L2K)

(no "Exon" information available for 5L2K)

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
                                                                                                                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eeeeeeeeee.....eeeeeeeee..eeeeeee....eeee.........hhhhhhhhhhhhhhhhhhhhhhhhhhh........eeeeeeeeeee.....eeeeeeeee..eeeeeee..eeee....hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeee.......eeeeeeeeeee....eeeeeee..ee....ee...eee...eeeeeeeeeee.......eeeeee.hhh...eeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5l2k A   4 FQGPTSFHVIQTSSFTNSTWAQTQGSGWLDDLQIHGWDSDSGTAIFLKPWSKGNFSDKEVAELEEIFRVYIFGFAREVQDFAGDFQMKYPFEIQGIAGCELHSGGAIVSFLRGALGGLDFLSVKNASCVPSPEGGSRAQKFCALIIQYQGIMETVRALLYETCPRYLLGVLNAGKADLQRQVKPEAWLSSGPSPGPGRLQLVCHVSGFYPKPVWVMWMRGEQEQQGTQLGDILPNANWTWYLRATLDVADGEAAGLSCRVKHSSLEGQDIILYWRG 279
                                    13        23        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

Chain B from PDB  Type:PROTEIN  Length:98
                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeee.........eeeeeeeeee.....eeeeee..ee....ee...ee.....eeeeeeeee.......eeeeee.......eeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------- Transcript
                 5l2k B   3 IQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDWSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRD 100
                                    12        22        32        42        52        62        72        82        92

Chain D from PDB  Type:PROTEIN  Length:185
                                                                                                                                                                                                                         
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee...eeeee....eeeeeeee......eeeeee......eeeeee.....eee..eeeeee....eeeeee...hhhhh.eeeeeee......eee...eeeeee........eeeeeee......eeeeeeee.............eee...eeee......eeeeeeeee......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5l2k D   1 GQNIDQPTEMTATEGAIVQINCTYQTSGFNGLFWYQQHAGEAPTFLSYNVLDGLEEKGRFSSFLSRSKGYSYLLLKELQMKDSASYLCAVRNTGGFKTIFGAGTRLFVKANIQNPDPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKSDFACAN 202
                                 || 11        21        31||      47        57  ||   |79     |||86        96       106 ||    117       127       137       147       157       167       177       187       197     
                                 6|                      32|                   60|  70|    84A||                     108|                                                                                            
                                  8                       39                    66   78     84B|                      110                                                                                            
                                                                                             84C

Chain E from PDB  Type:PROTEIN  Length:242
                                                                                                                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee..eeeee....eeeeeee.....eeeeeeee...eeeeeeee......ee......eeeeeee..eeeeee...hhhhh.eeeeeee........ee...eeeeee.hhhhh...eeeeee.hhhhhhhhheeeeeeeeeee....eeeeeee..eee...eee....ee.........eeeeeeeeeehhhhhh...eeeeeeee..................eeeeeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5l2k E   2 AGVTQTPKFRVLKTGQSMTLLCAQDMNHEYMYWYRQDPGMGLRLIHYSVGEGTTAKGEVPDGYNVSRLKKQNFLLGLESAAPSQTSVYFCASSPRLAGDEQFFGPGTRLTVLEDLKNVFPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQPALNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGRAD 256
                                    11        21        31|       48        58  ||    72|      |84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254  
                                                        31|                    61|    72|     81|                                                                                                                                                                             
                                                         39                     66     74      83

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 5L2K)

(no "CATH Domain" information available for 5L2K)

(no "Pfam Domain" information available for 5L2K)

Asymmetric Unit(hide GO term definitions)

Asymmetric Unit
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	Ligands, Modified Residues, Ions
		6UL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		70E	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		CL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
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	Cis Peptide Bonds
		Ala D:46 - Gly D:47	[ RasMol ]
		Asp D:59 - Gly D:60	[ RasMol ]
		Asp E:74 - Gly E:75	[ RasMol ]
		Gln D:158 - Thr D:159	[ RasMol ]
		Gly E:112 - Asp E:113	[ RasMol ]
		Gly E:47 - Met E:48	[ RasMol ]
		His B:33 - Pro B:34	[ RasMol ]
		Lys D:143 - Ser D:144	[ RasMol ]
		Thr D:110 - Gly D:111	[ RasMol ]
		Thr E:7 - Pro E:8	[ RasMol ]
		Tyr A:212 - Pro A:213	[ RasMol ]
		Tyr A:92 - Pro A:93	[ RasMol ]
		Tyr E:163 - Pro E:164	[ RasMol ]

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

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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (7, 17)

Sites (15, 15)

SS Bonds (9, 9)

Cis Peptide Bonds (13, 13)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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