PDB-1n5a: Crystal structure of the Murine class I Major Histocompatibility ...

ID or keywords:

Entry

Database: PDB / ID: 1n5a

Title

Crystal structure of the Murine class I Major Histocompatibility Complex of H-2DB, B2-Microglobulin, and A 9-Residue immunodominant peptide epitope gp33 derived from LCMV

Components

Beta-2-microglobulin
H-2 class I histocompatibility antigen, D-B alpha chain
nonameric peptide, gp33 derived from lymphocytic choriomeningitis virus

Keywords

IMMUNE SYSTEM / Murine MHC / viral escape / LCMV / immunodominant epitope

Function / homology

Function and homology information

Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / host cell Golgi membrane / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / beta-2-microglobulin binding / cellular defense response ...Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / host cell Golgi membrane / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / beta-2-microglobulin binding / cellular defense response / Neutrophil degranulation / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / lumenal side of endoplasmic reticulum membrane / peptide binding / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / multicellular organismal-level iron ion homeostasis / negative regulation of neurogenesis / peptide antigen assembly with MHC class II protein complex / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / phagocytic vesicle membrane / positive regulation of cellular senescence / peptide antigen binding / negative regulation of epithelial cell proliferation / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / sensory perception of smell / positive regulation of T cell activation / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / iron ion transport / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / receptor-mediated endocytosis of virus by host cell / learning or memory / host cell endoplasmic reticulum membrane / immune response / lysosomal membrane / external side of plasma membrane / signaling receptor binding / fusion of virus membrane with host endosome membrane / viral envelope / protein-containing complex binding / virion attachment to host cell / host cell plasma membrane / structural molecule activity / virion membrane / Golgi apparatus / protein homodimerization activity / extracellular space / membrane / metal ion binding / plasma membrane / cytosol
Similarity search - Function

Biological species

Mus musculus (house mouse)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.85 Å

Authors

Achour, A. / Michaelsson, J. / Harris, R.A. / Odeberg, J. / Grufman, P. / Sandberg, J.K. / Levitsky, V. / Karre, K. / Sandalova, T. / Schneider, G.

Citation

Journal: Immunity / Year: 2002
Title: A Structural Basis for LCMV Immune Evasion. Subversion of H-2D(b) and H-2K(b) Presentation of gp33 Revealed by Comparative Crystal Structure Analyses.
Authors: Achour, A. / Michaelsson, J. / Harris, R.A. / Odeberg, J. / Grufman, P. / Sandberg, J.K. / Levitsky, V. / Karre, K. / Sandalova, T. / Schneider, G.

History

Deposition	Nov 5, 2002	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 7, 2003	Provider: repository / Type: Initial release
Revision 1.1	Apr 28, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.3	Mar 7, 2018	Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4	Oct 27, 2021	Group: Database references / Category: database_2 / struct_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	1n5a.cif.gz	311.1 KB	Display	PDBx/mmCIF format
PDB format	pdb1n5a.ent.gz	264.7 KB	Display	PDB format
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Validation report

Summary document	1n5a_validation.pdf.gz	514.4 KB	Display	wwPDB validaton report
Full document	1n5a_full_validation.pdf.gz	590.2 KB	Display
Data in XML	1n5a_validation.xml.gz	62.3 KB	Display
Data in CIF	1n5a_validation.cif.gz	83.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/n5/1n5a ftp://data.pdbj.org/pub/pdb/validation_reports/n5/1n5a	HTTPS FTP

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Related structure data

Related structure data	1n59C 1hocS 1fg2 S: Starting model for refinement C: citing same article (ref.)
Similar structure data	7lgd-1 3rwd-1 3v5k-1 3v5d-1 4l8d-1 4nqv-5 3tbw-2 5bxf-1 3vfs-d 6l9n-3 3bvn-1 1n3n-3 1s7w-1 6gb7-4 1uxs-d 6lf9-1 6gl1-2 6y28-d 5w6a-2 6vb1-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

1n59C

1hocS

1fg2

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#62 - Feb 2005 Major Histocompatibility Complex similarity (10) #63 - Mar 2005 T-Cell Receptor similarity (10) #21 - Sep 2001 Antibodies similarity (1) #182 - Feb 2015 Insulin receptor similarity (1) #80 - Aug 2006 AAA+ Proteases similarity (1) #88 - Apr 2007 Clathrin similarity (1) #143 - Nov 2011 Toll-like Receptors similarity (1) #166 - Oct 2013 Proteasome similarity (1) #176 - Aug 2014 Dynein similarity (1) #177 - Sep 2014 Apoptosomes similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#62 - Feb 2005
Major Histocompatibility Complex
similarity (10)
#63 - Mar 2005
T-Cell Receptor
similarity (10)
#21 - Sep 2001
Antibodies
similarity (1)
#182 - Feb 2015
Insulin receptor
similarity (1)
#80 - Aug 2006
AAA+ Proteases
similarity (1)
#88 - Apr 2007
Clathrin
similarity (1)
#143 - Nov 2011
Toll-like Receptors
similarity (1)
#166 - Oct 2013
Proteasome
similarity (1)
#176 - Aug 2014
Dynein
similarity (1)
#177 - Sep 2014
Apoptosomes
similarity (1)

Deposited unit

A: H-2 class I histocompatibility antigen, D-B alpha chain

B: Beta-2-microglobulin

C: nonameric peptide, gp33 derived from lymphocytic choriomeningitis virus

D: H-2 class I histocompatibility antigen, D-B alpha chain

E: Beta-2-microglobulin

F: nonameric peptide, gp33 derived from lymphocytic choriomeningitis virus

G: H-2 class I histocompatibility antigen, D-B alpha chain

H: Beta-2-microglobulin

I: nonameric peptide, gp33 derived from lymphocytic choriomeningitis virus

J: H-2 class I histocompatibility antigen, D-B alpha chain

K: Beta-2-microglobulin

L: nonameric peptide, gp33 derived from lymphocytic choriomeningitis virus

179 kDa, 12 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: H-2 class I histocompatibility antigen, D-B alpha chain

B: Beta-2-microglobulin

C: nonameric peptide, gp33 derived from lymphocytic choriomeningitis virus

defined by author&software
44.8 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

D: H-2 class I histocompatibility antigen, D-B alpha chain

E: Beta-2-microglobulin

F: nonameric peptide, gp33 derived from lymphocytic choriomeningitis virus

defined by author&software
44.8 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

G: H-2 class I histocompatibility antigen, D-B alpha chain

H: Beta-2-microglobulin

I: nonameric peptide, gp33 derived from lymphocytic choriomeningitis virus

defined by author&software
44.8 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

J: H-2 class I histocompatibility antigen, D-B alpha chain

K: Beta-2-microglobulin

L: nonameric peptide, gp33 derived from lymphocytic choriomeningitis virus

defined by author&software
44.8 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	91.998, 122.657, 99.180
Angle α, β, γ (deg.)	90.00, 103.34, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Beg label comp-ID	End label comp-ID	Refine code	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	HIS	SER	1	A	A	3 - 13	3 - 13
2	1	1	HIS	SER	1	D	D	3 - 13	3 - 13
3	1	1	HIS	SER	1	G	G	3 - 13	3 - 13
4	1	1	HIS	SER	1	J	J	3 - 13	3 - 13
5	2	1	PRO	VAL	1	A	A	20 - 28	20 - 28
6	2	1	PRO	VAL	1	D	D	20 - 28	20 - 28
7	2	1	PRO	VAL	1	G	G	20 - 28	20 - 28
8	2	1	PRO	VAL	1	J	J	20 - 28	20 - 28
9	3	1	ASP	ASN	3	A	A	29 - 30	29 - 30
10	3	1	ASP	ASN	3	D	D	29 - 30	29 - 30
11	3	1	ASP	ASN	3	G	G	29 - 30	29 - 30
12	3	1	ASP	ASN	3	J	J	29 - 30	29 - 30
13	4	1	LYS	ALA	1	A	A	31 - 40	31 - 40
14	4	1	LYS	ALA	1	D	D	31 - 40	31 - 40
15	4	1	LYS	ALA	1	G	G	31 - 40	31 - 40
16	4	1	LYS	ALA	1	J	J	31 - 40	31 - 40
17	5	1	GLU	GLU	3	A	A	41	41
18	5	1	GLU	GLU	3	D	D	41	41
19	5	1	GLU	GLU	3	G	G	41	41
20	5	1	GLU	GLU	3	J	J	41	41
21	6	1	ASN	PRO	1	A	A	42 - 43	42 - 43
22	6	1	ASN	PRO	1	D	D	42 - 43	42 - 43
23	6	1	ASN	PRO	1	G	G	42 - 43	42 - 43
24	6	1	ASN	PRO	1	J	J	42 - 43	42 - 43
25	7	1	ARG	ARG	3	A	A	44	44
26	7	1	ARG	ARG	3	D	D	44	44
27	7	1	ARG	ARG	3	G	G	44	44
28	7	1	ARG	ARG	3	J	J	44	44
29	8	1	TYR	MET	1	A	A	45 - 52	45 - 52
30	8	1	TYR	MET	1	D	D	45 - 52	45 - 52
31	8	1	TYR	MET	1	G	G	45 - 52	45 - 52
32	8	1	TYR	MET	1	J	J	45 - 52	45 - 52
33	9	1	GLU	GLU	3	A	A	53	53
34	9	1	GLU	GLU	3	D	D	53	53
35	9	1	GLU	GLU	3	G	G	53	53
36	9	1	GLU	GLU	3	J	J	53	53
37	10	1	GLN	PRO	1	A	A	54 - 57	54 - 57
38	10	1	GLN	PRO	1	D	D	54 - 57	54 - 57
39	10	1	GLN	PRO	1	G	G	54 - 57	54 - 57
40	10	1	GLN	PRO	1	J	J	54 - 57	54 - 57
1	1	2	GLU	GLU	3	A	A	58	58
2	1	2	GLU	GLU	3	D	D	58	58
3	1	2	GLU	GLU	3	G	G	58	58
4	1	2	GLU	GLU	3	J	J	58	58
5	2	2	TYR	GLN	1	A	A	59 - 65	59 - 65
6	2	2	TYR	GLN	1	D	D	59 - 65	59 - 65
7	2	2	TYR	GLN	1	G	G	59 - 65	59 - 65
8	2	2	TYR	GLN	1	J	J	59 - 65	59 - 65
9	3	2	LYS	LYS	3	A	A	66	66
10	3	2	LYS	LYS	3	D	D	66	66
11	3	2	LYS	LYS	3	G	G	66	66
12	3	2	LYS	LYS	3	J	J	66	66
13	4	2	ALA	GLU	1	A	A	67 - 71	67 - 71
14	4	2	ALA	GLU	1	D	D	67 - 71	67 - 71
15	4	2	ALA	GLU	1	G	G	67 - 71	67 - 71
16	4	2	ALA	GLU	1	J	J	67 - 71	67 - 71
17	5	2	GLN	GLN	3	A	A	72	72
18	5	2	GLN	GLN	3	D	D	72	72
19	5	2	GLN	GLN	3	G	G	72	72
20	5	2	GLN	GLN	3	J	J	72	72
21	6	2	TRP	PHE	1	A	A	73 - 74	73 - 74
22	6	2	TRP	PHE	1	D	D	73 - 74	73 - 74
23	6	2	TRP	PHE	1	G	G	73 - 74	73 - 74
24	6	2	TRP	PHE	1	J	J	73 - 74	73 - 74
25	7	2	ARG	ARG	3	A	A	75	75
26	7	2	ARG	ARG	3	D	D	75	75
27	7	2	ARG	ARG	3	G	G	75	75
28	7	2	ARG	ARG	3	J	J	75	75
29	8	2	VAL	LEU	1	A	A	76 - 78	76 - 78
30	8	2	VAL	LEU	1	D	D	76 - 78	76 - 78
31	8	2	VAL	LEU	1	G	G	76 - 78	76 - 78
32	8	2	VAL	LEU	1	J	J	76 - 78	76 - 78
33	9	2	ARG	ARG	3	A	A	79	79
34	9	2	ARG	ARG	3	D	D	79	79
35	9	2	ARG	ARG	3	G	G	79	79
36	9	2	ARG	ARG	3	J	J	79	79
1	1	3	GLY	TRP	1	A	A	83 - 107	83 - 107
2	1	3	GLY	TRP	1	D	D	83 - 107	83 - 107
3	1	3	GLY	TRP	1	G	G	83 - 107	83 - 107
4	1	3	GLY	TRP	1	J	J	83 - 107	83 - 107
5	2	3	ARG	ARG	3	A	A	108	108
6	2	3	ARG	ARG	3	D	D	108	108
7	2	3	ARG	ARG	3	G	G	108	108
8	2	3	ARG	ARG	3	J	J	108	108
9	3	3	LEU	LEU	1	A	A	109 - 110	109 - 110
10	3	3	LEU	LEU	1	D	D	109 - 110	109 - 110
11	3	3	LEU	LEU	1	G	G	109 - 110	109 - 110
12	3	3	LEU	LEU	1	J	J	109 - 110	109 - 110
13	4	3	ARG	ARG	3	A	A	111	111
14	4	3	ARG	ARG	3	D	D	111	111
15	4	3	ARG	ARG	3	G	G	111	111
16	4	3	ARG	ARG	3	J	J	111	111
17	5	3	GLY	ALA	1	A	A	112 - 139	112 - 139
18	5	3	GLY	ALA	1	D	D	112 - 139	112 - 139
19	5	3	GLY	ALA	1	G	G	112 - 139	112 - 139
20	5	3	GLY	ALA	1	J	J	112 - 139	112 - 139
21	6	3	ALA	THR	1	A	A	140 - 143	140 - 143
22	6	3	ALA	THR	1	D	D	140 - 143	140 - 143
23	6	3	ALA	THR	1	G	G	140 - 143	140 - 143
24	6	3	ALA	THR	1	J	J	140 - 143	140 - 143
25	7	3	ARG	LYS	3	A	A	144 - 146	144 - 146
26	7	3	ARG	LYS	3	D	D	144 - 146	144 - 146
27	7	3	ARG	LYS	3	G	G	144 - 146	144 - 146
28	7	3	ARG	LYS	3	J	J	144 - 146	144 - 146
29	8	3	TRP	GLU	1	A	A	147 - 148	147 - 148
30	8	3	TRP	GLU	1	D	D	147 - 148	147 - 148
31	8	3	TRP	GLU	1	G	G	147 - 148	147 - 148
32	8	3	TRP	GLU	1	J	J	147 - 148	147 - 148
1	1	4	GLN	GLN	3	A	A	149	149
2	1	4	GLN	GLN	3	D	D	149	149
3	1	4	GLN	GLN	3	G	G	149	149
4	1	4	GLN	GLN	3	J	J	149	149
5	2	4	SER	GLU	1	A	A	150 - 154	150 - 154
6	2	4	SER	GLU	1	D	D	150 - 154	150 - 154
7	2	4	SER	GLU	1	G	G	150 - 154	150 - 154
8	2	4	SER	GLU	1	J	J	150 - 154	150 - 154
9	3	4	HIS	HIS	3	A	A	155	155
10	3	4	HIS	HIS	3	D	D	155	155
11	3	4	HIS	HIS	3	G	G	155	155
12	3	4	HIS	HIS	3	J	J	155	155
13	4	4	TYR	VAL	1	A	A	156 - 165	156 - 165
14	4	4	TYR	VAL	1	D	D	156 - 165	156 - 165
15	4	4	TYR	VAL	1	G	G	156 - 165	156 - 165
16	4	4	TYR	VAL	1	J	J	156 - 165	156 - 165
17	5	4	TRP	HIS	1	A	A	167 - 169	167 - 169
18	5	4	TRP	HIS	1	D	D	167 - 169	167 - 169
19	5	4	TRP	HIS	1	G	G	167 - 169	167 - 169
20	5	4	TRP	HIS	1	J	J	167 - 169	167 - 169
21	6	4	ARG	ARG	3	A	A	170	170
22	6	4	ARG	ARG	3	D	D	170	170
23	6	4	ARG	ARG	3	G	G	170	170
24	6	4	ARG	ARG	3	J	J	170	170
25	7	4	TYR	ASN	1	A	A	171 - 174	171 - 174
26	7	4	TYR	ASN	1	D	D	171 - 174	171 - 174
27	7	4	TYR	ASN	1	G	G	171 - 174	171 - 174
28	7	4	TYR	ASN	1	J	J	171 - 174	171 - 174
29	8	4	ASP	LYS	6	A	A	183 - 186	183 - 186
30	8	4	ASP	LYS	6	D	D	183 - 186	183 - 186
31	8	4	ASP	LYS	6	G	G	183 - 186	183 - 186
32	8	4	ASP	LYS	6	J	J	183 - 186	183 - 186
1	1	5	ALA	HIS	1	A	A	187 - 192	187 - 192
2	1	5	ALA	HIS	1	D	D	187 - 192	187 - 192
3	1	5	ALA	HIS	1	G	G	187 - 192	187 - 192
4	1	5	ALA	HIS	1	J	J	187 - 192	187 - 192
5	2	5	THR	GLN	1	A	A	200 - 218	200 - 218
6	2	5	THR	GLN	1	D	D	200 - 218	200 - 218
7	2	5	THR	GLN	1	G	G	200 - 218	200 - 218
8	2	5	THR	GLN	1	J	J	200 - 218	200 - 218
9	3	5	LEU	GLN	1	A	A	224 - 226	224 - 226
10	3	5	LEU	GLN	1	D	D	224 - 226	224 - 226
11	3	5	LEU	GLN	1	G	G	224 - 226	224 - 226
12	3	5	LEU	GLN	1	J	J	224 - 226	224 - 226
13	4	5	ASP	GLU	3	A	A	227 - 229	227 - 229
14	4	5	ASP	GLU	3	D	D	227 - 229	227 - 229
15	4	5	ASP	GLU	3	G	G	227 - 229	227 - 229
16	4	5	ASP	GLU	3	J	J	227 - 229	227 - 229
17	5	5	LEU	VAL	1	A	A	230 - 231	230 - 231
18	5	5	LEU	VAL	1	D	D	230 - 231	230 - 231
19	5	5	LEU	VAL	1	G	G	230 - 231	230 - 231
20	5	5	LEU	VAL	1	J	J	230 - 231	230 - 231
21	6	5	GLU	GLU	3	A	A	232	232
22	6	5	GLU	GLU	3	D	D	232	232
23	6	5	GLU	GLU	3	G	G	232	232
24	6	5	GLU	GLU	3	J	J	232	232
25	7	5	THR	VAL	1	A	A	233 - 249	233 - 249
26	7	5	THR	VAL	1	D	D	233 - 249	233 - 249
27	7	5	THR	VAL	1	G	G	233 - 249	233 - 249
28	7	5	THR	VAL	1	J	J	233 - 249	233 - 249
29	8	5	TYR	CYS	1	A	A	257 - 259	257 - 259
30	8	5	TYR	CYS	1	D	D	257 - 259	257 - 259
31	8	5	TYR	CYS	1	G	G	257 - 259	257 - 259
32	8	5	TYR	CYS	1	J	J	257 - 259	257 - 259
1	1	6	ARG	ARG	3	A	A	260	260
2	1	6	ARG	ARG	3	D	D	260	260
3	1	6	ARG	ARG	3	G	G	260	260
4	1	6	ARG	ARG	3	J	J	260	260
5	2	6	VAL	HIS	1	A	A	261 - 263	261 - 263
6	2	6	VAL	HIS	1	D	D	261 - 263	261 - 263
7	2	6	VAL	HIS	1	G	G	261 - 263	261 - 263
8	2	6	VAL	HIS	1	J	J	261 - 263	261 - 263
9	3	6	GLU	GLU	6	A	A	264	264
10	3	6	GLU	GLU	6	D	D	264	264
11	3	6	GLU	GLU	6	G	G	264	264
12	3	6	GLU	GLU	6	J	J	264	264
13	4	6	GLY	LEU	1	A	A	265 - 272	265 - 272
14	4	6	GLY	LEU	1	D	D	265 - 272	265 - 272
15	4	6	GLY	LEU	1	G	G	265 - 272	265 - 272
16	4	6	GLY	LEU	1	J	J	265 - 272	265 - 272
1	1	7	GLN	PRO	1	B	B	2 - 15	2 - 15
2	1	7	GLN	PRO	1	E	E	2 - 15	2 - 15
3	1	7	GLN	PRO	1	H	H	2 - 15	2 - 15
4	1	7	GLN	PRO	1	K	K	2 - 15	2 - 15
5	2	7	GLU	GLU	3	B	B	16	16
6	2	7	GLU	GLU	3	E	E	16	16
7	2	7	GLU	GLU	3	H	H	16	16
8	2	7	GLU	GLU	3	K	K	16	16
9	3	7	ASN	GLY	1	B	B	17 - 18	17 - 18
10	3	7	ASN	GLY	1	E	E	17 - 18	17 - 18
11	3	7	ASN	GLY	1	H	H	17 - 18	17 - 18
12	3	7	ASN	GLY	1	K	K	17 - 18	17 - 18
13	4	7	LYS	LYS	3	B	B	19	19
14	4	7	LYS	LYS	3	E	E	19	19
15	4	7	LYS	LYS	3	H	H	19	19
16	4	7	LYS	LYS	3	K	K	19	19
17	5	7	PRO	PRO	1	B	B	20 - 47	20 - 47
18	5	7	PRO	PRO	1	E	E	20 - 47	20 - 47
19	5	7	PRO	PRO	1	H	H	20 - 47	20 - 47
20	5	7	PRO	PRO	1	K	K	20 - 47	20 - 47
21	6	7	LYS	LYS	3	B	B	48	48
22	6	7	LYS	LYS	3	E	E	48	48
23	6	7	LYS	LYS	3	H	H	48	48
24	6	7	LYS	LYS	3	K	K	48	48
25	7	7	VAL	SER	1	B	B	49 - 57	49 - 57
26	7	7	VAL	SER	1	E	E	49 - 57	49 - 57
27	7	7	VAL	SER	1	H	H	49 - 57	49 - 57
28	7	7	VAL	SER	1	K	K	49 - 57	49 - 57
29	8	7	LYS	LYS	3	B	B	58	58
30	8	7	LYS	LYS	3	E	E	58	58
31	8	7	LYS	LYS	3	H	H	58	58
32	9	7	ASP	ALA	1	K	K	59 - 88	59 - 88
33	10	7	GLU	LYS	3	B	B	89 - 91	89 - 91
34	10	7	GLU	LYS	3	E	E	89 - 91	89 - 91
35	10	7	GLU	LYS	3	H	H	89 - 91	89 - 91
36	10	7	GLU	LYS	3	K	K	89 - 91	89 - 91
37	11	7	THR	ASP	1	B	B	92 - 98	92 - 98
38	11	7	THR	ASP	1	E	E	92 - 98	92 - 98
39	11	7	THR	ASP	1	H	H	92 - 98	92 - 98
40	11	7	THR	ASP	1	K	K	92 - 98	92 - 98
1	1	8	LYS	MET	6	C	C	1 - 9	1 - 9
2	1	8	LYS	MET	6	F	F	1 - 9	1 - 9
3	1	8	LYS	MET	6	I	I	1 - 9	1 - 9
4	1	8	LYS	MET	6	L	L	1 - 9	1 - 9

NCS ensembles :

ID
1
2
3
4
5
6
7
8

#1: Protein	H-2 class I histocompatibility antigen, D-B alpha chain / H-2DB Mass: 32087.703 Da / Num. of mol.: 4 / Fragment: Extracellular part Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-D / Production host: Escherichia coli (E. coli) / References: UniProt: P01899
#2: Protein	Beta-2-microglobulin Mass: 11704.359 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: B2M / Production host: Escherichia coli (E. coli) / References: UniProt: P01887
#3: Protein/peptide	nonameric peptide, gp33 derived from lymphocytic choriomeningitis virus Mass: 1045.232 Da / Num. of mol.: 4 / Mutation: C9M / Source method: obtained synthetically / Details: THE PEPTIDE WAS CHEMICALLY SYNTHESIZED / References: UniProt: Q9QDK7
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 65 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

Crystal

Density Matthews: 3.08 Å³/Da / Density % sol: 59.73 %

Crystal grow

Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: Ammonium sulfate, ethylene glycol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

Crystal grow

*PLUS

pH: 7

Components of the solutions

*PLUS

ID	Conc.	Common name	Crystal-ID	Sol-ID	Details
1	1.8 M	ammonium sulfate	1	reservoir
2	0.1 M	Tris-Cl	1	reservoir	pH8.5
3	3-4 %	ethylene glycol	1	reservoir
4	6 mg/ml	protein	1	drop
5	20 mM	Tris-Cl	1	drop	pH7.0

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.0292 Å
Detector	Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 28, 2000
Radiation	Monochromator: Si(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.0292 Å / Relative weight: 1
Reflection	Resolution: 2.85→20 Å / Num. all: 46560 / Num. obs: 46560 / % possible obs: 92.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.9 % / B_iso Wilson estimate: 63.9 Å² / R_sym value: 0.096 / Net I/σ(I): 12
Reflection shell	Resolution: 2.85→2.9 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 9.8 / Num. unique all: 2453 / R_sym value: 0.254 / % possible all: 94.4
Reflection	PLUS Lowest resolution: 20 Å / Num. measured all: 135354 / R_merge(I) obs*: 0.096
Reflection shell	PLUS % possible obs: 98 % / R_merge(I) obs*: 0.254

-
Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
AMoRE		phasing
REFMAC	5	refinement

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HOC

1hoc

Resolution: 2.85→19.92 Å / Cor.coef. F_o:F_c: 0.868 / Cor.coef. F_o:F_c free: 0.835 / SU B: 16.738 / SU ML: 0.338 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: TLS / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.438

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.27861	2277	5 %	RANDOM
R_work	0.25128	-	-	-
all	0.2526	43227	-	-
obs	0.25264	43227	100 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 11.109 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.34 Å²	0 Å²	-2.6 Å²
2-	-	1.53 Å²	0 Å²
3-	-	-	-2.39 Å²

Refinement step

Cycle: LAST / Resolution: 2.85→19.92 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	12568	0	0	65	12633

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.031	0.021	12956
X-RAY DIFFRACTION	r_angle_refined_deg	2.282	1.93	17585
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.38	3	1515
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	22.018	15	2288
X-RAY DIFFRACTION	r_chiral_restr	0.133	0.2	1773
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.02	10168
X-RAY DIFFRACTION	r_nbd_refined	0.31	0.3	6353
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.179	0.5	1223
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.428	0.3	157
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.355	0.5	16
X-RAY DIFFRACTION	r_mcbond_it	0.672	1.5	7633
X-RAY DIFFRACTION	r_mcangle_it	1.305	2	12310
X-RAY DIFFRACTION	r_scbond_it	1.912	3	5323
X-RAY DIFFRACTION	r_scangle_it	3.298	4.5	5275

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-ID	Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	1	A	392	tight positional	0.27	0.05
1	2	D	392	tight positional	0.24	0.05
1	3	G	392	tight positional	0.18	0.05
1	4	J	392	tight positional	0.16	0.05
2	1	A	594	tight positional	0.38	0.05
2	2	D	594	tight positional	0.43	0.05
2	3	G	594	tight positional	0.44	0.05
2	4	J	594	tight positional	0.36	0.05
3	1	A	1127	tight positional	0.15	0.05
3	2	D	1127	tight positional	0.1	0.05
3	3	G	1127	tight positional	0.11	0.05
3	4	J	1127	tight positional	0.12	0.05
4	1	A	1366	tight positional	0.11	0.05
4	2	D	1366	tight positional	0.12	0.05
4	3	G	1366	tight positional	0.13	0.05
4	4	J	1366	tight positional	0.2	0.05
5	1	A	1800	tight positional	0.15	0.05
5	2	D	1800	tight positional	0.14	0.05
5	3	G	1800	tight positional	0.1	0.05
5	4	J	1800	tight positional	0.09	0.05
6	1	A	1907	tight positional	0.08	0.05
6	2	D	1907	tight positional	0.09	0.05
6	3	G	1907	tight positional	0.06	0.05
6	4	J	1907	tight positional	0.05	0.05
7	1	B	2711	tight positional	0.09	0.05
7	2	E	2711	tight positional	0.05	0.05
7	3	H	2711	tight positional	0.06	0.05
7	4	K	2711	tight positional	0.05	0.05
8	1	C	2784	tight positional	0.06	0.05
8	2	F	2784	tight positional	0.11	0.05
8	3	I	2784	tight positional	0.09	0.05
8	4	L	2784	tight positional	0.07	0.05
1	1	A	21	loose positional	0.17	5
1	2	D	21	loose positional	0.15	5
1	3	G	21	loose positional	0.12	5
1	4	J	21	loose positional	0.14	5
2	1	A	21	loose positional	0.09	5
2	2	D	21	loose positional	0.09	5
2	3	G	21	loose positional	0.07	5
2	4	J	21	loose positional	0.08	5
3	1	A	21	loose positional	0.07	5
3	2	D	21	loose positional	0.06	5
3	3	G	21	loose positional	0.06	5
3	4	J	21	loose positional	0.06	5
4	1	A	21	loose positional	0.06	5
4	2	D	21	loose positional	0.06	5
4	3	G	21	loose positional	0.05	5
4	4	J	21	loose positional	0.05	5
5	1	A	21	loose positional	0.05	5
5	2	D	21	loose positional	0.05	5
5	3	G	21	loose positional	0.05	5
5	4	J	21	loose positional	0.05	5
6	1	A	21	loose positional	0.05	5
6	2	D	21	loose positional	0.05	5
6	3	G	21	loose positional	0.05	5
6	4	J	21	loose positional	0.05	5
7	1	B	21	loose positional	0.05	5
7	2	E	21	loose positional	0.05	5
7	3	H	21	loose positional	0.05	5
7	4	K	21	loose positional	0.05	5
8	1	C	21	loose positional	0.05	5
8	2	F	21	loose positional	0.05	5
8	3	I	21	loose positional	0.05	5
8	4	L	21	loose positional	0.05	5
1	1	A	392	tight thermal	0.13	0.5
1	2	D	392	tight thermal	0.15	0.5
1	3	G	392	tight thermal	0.13	0.5
1	4	J	392	tight thermal	0.14	0.5
2	1	A	594	tight thermal	1.19	0.5
2	2	D	594	tight thermal	1.25	0.5
2	3	G	594	tight thermal	1.16	0.5
2	4	J	594	tight thermal	1.2	0.5
3	1	A	1127	tight thermal	2.57	0.5
3	2	D	1127	tight thermal	2.63	0.5
3	3	G	1127	tight thermal	2.54	0.5
3	4	J	1127	tight thermal	2.58	0.5
4	1	A	1366	tight thermal	3.43	0.5
4	2	D	1366	tight thermal	3.46	0.5
4	3	G	1366	tight thermal	3.4	0.5
4	4	J	1366	tight thermal	3.43	0.5
5	1	A	1800	tight thermal	3.44	0.5
5	2	D	1800	tight thermal	3.46	0.5
5	3	G	1800	tight thermal	3.43	0.5
5	4	J	1800	tight thermal	3.45	0.5
6	1	A	1907	tight thermal	3.36	0.5
6	2	D	1907	tight thermal	3.37	0.5
6	3	G	1907	tight thermal	3.35	0.5
6	4	J	1907	tight thermal	3.36	0.5
7	1	B	2711	tight thermal	2.78	0.5
7	2	E	2711	tight thermal	2.78	0.5
7	3	H	2711	tight thermal	2.78	0.5
7	4	K	2711	tight thermal	2.78	0.5
8	1	C	2784	tight thermal	2.49	0.5
8	2	F	2784	tight thermal	2.5	0.5
8	3	I	2784	tight thermal	2.49	0.5
8	4	L	2784	tight thermal	2.5	0.5
1	1	A	21	loose thermal	1.81	10
1	2	D	21	loose thermal	1.61	10
1	3	G	21	loose thermal	2.99	10
1	4	J	21	loose thermal	1.44	10
2	1	A	21	loose thermal	23.18	10
2	2	D	21	loose thermal	21.88	10
2	3	G	21	loose thermal	29.81	10
2	4	J	21	loose thermal	20.66	10
3	1	A	21	loose thermal	82.96	10
3	2	D	21	loose thermal	80.6	10
3	3	G	21	loose thermal	94.07	10
3	4	J	21	loose thermal	78.32	10
4	1	A	21	loose thermal		10
4	2	D	21	loose thermal		10
4	3	G	21	loose thermal		10
4	4	J	21	loose thermal		10
5	1	A	21	loose thermal		10
5	2	D	21	loose thermal		10
5	3	G	21	loose thermal		10
5	4	J	21	loose thermal		10
6	1	A	21	loose thermal		10
6	2	D	21	loose thermal		10
6	3	G	21	loose thermal		10
6	4	J	21	loose thermal		10
7	1	B	21	loose thermal		10
7	2	E	21	loose thermal		10
7	3	H	21	loose thermal		10
7	4	K	21	loose thermal		10
8	1	C	21	loose thermal		10
8	2	F	21	loose thermal		10
8	3	I	21	loose thermal		10
8	4	L	21	loose thermal		10

LS refinement shell

Resolution: 2.85→2.922 Å / Total num. of bins used: 20 /

	R_factor	Num. reflection
R_free	0.376	146
R_work	0.313	3204

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	2.1488	-0.3333	0.6446	1.4622	0.4155	2.1229	0.0614	0.1427	-0.0399	0.2995	-0.0167	-0.2761	0.1479	0.4298	-0.0446	0.223	-0.0765	0.1033	0.3426	0.0193	0.4295	-5.17	-2.968	25.896
2	3.5635	1.1666	3.9475	4.2004	3.4412	6.4711	-0.1386	0.0817	0.1029	-0.1815	0.1718	0.0838	-0.363	0.0628	-0.0332	0.1371	-0.105	0.1343	0.3945	0.0541	0.2561	-2.738	10.696	40.333
3	25.378	-8.1144	3.8234	3.9255	-0.8202	0.096	0.34	0.5698	1.1036	-0.7213	-0.7229	-0.3491	0.1676	0.4085	0.3829	0.3164	-0.0408	0.215	0.5278	0.2317	0.2749	-13.62	0.307	7.695
4	0.4573	0.2966	0.6183	1.2213	-0.0296	2.8327	0.0439	0.1821	-0.0867	0.1116	0.021	-0.2925	0.1561	0.5144	-0.0649	0.1869	-0.0127	0.1062	0.3651	-0.0532	0.3844	30.998	56.248	74.911
5	2.19	1.4896	2.9257	4.433	2.5361	7.1749	-0.0548	0.1782	0.0874	0.0962	0.1636	-0.2534	-0.5336	0.5734	-0.1087	0.2381	-0.083	0.18	0.3858	-0.0432	0.2352	34.648	69.627	89.321
6	33.3649	-8.271	3.3703	7.8424	0.1379	2.6091	-0.0496	2.0398	1.2777	-0.6834	-0.1241	-0.2388	0.2598	0.5179	0.1736	0.2713	-0.1322	0.1446	0.4364	0.0725	0.1442	23.717	60.863	56.799
7	3.4912	0.1215	-0.9127	3.1011	0.3947	2.4169	0.0921	0.0744	0.2563	-0.3244	0.0307	-0.6531	-0.017	0.541	-0.1228	0.216	0.0819	0.0985	0.3938	-0.0043	0.3877	-3.442	86.656	24.481
8	6.0463	-2.1595	-5.4938	2.4063	3.9214	7.1399	0.0912	0.1537	-0.4565	0.0387	0.0896	-0.139	0.2568	0.0279	-0.1809	0.3158	0.1228	0.0387	0.3999	-0.0163	0.3953	1.796	72.418	11.182
9	3.5351	10.0436	-8.664	8.0377	0.0954	-5.1287	1.0758	-3.089	-1.7138	0.6893	-1.2002	-0.6922	-0.014	0.9304	0.1244	0.2922	-0.0053	-0.0691	0.6149	0.1233	0.2693	-12.72	83.058	41.658
10	2.7811	0.7006	-0.6825	2.5104	0.2681	1.4335	-0.072	0.0208	-0.0125	0.0814	0.2465	-0.6373	-0.0309	0.3131	-0.1744	0.2324	0.1308	-0.0077	0.2832	-0.0885	0.3895	29.265	23.183	72.776
11	4.1758	-1.6838	-4.1673	1.6186	1.6585	6.2953	-0.1726	0.0461	-0.1338	0.1659	0.2403	-0.2794	0.5139	0.1414	-0.0677	0.2245	0.0792	0.0473	0.3626	-0.0907	0.312	33.392	9.565	58.822
12	50.4747	22.7172	-8.1796	9.5466	0.1284	-6.7831	1.1061	-2.8336	-1.7215	1.6552	-0.6715	-0.2798	-0.1386	0.4534	-0.4345	0.606	0.187	-0.0211	0.4027	0.1126	0.2072	19.681	19.147	89.807

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	X-RAY DIFFRACTION	1	A	A	2 - 182	2 - 182
2	X-RAY DIFFRACTION	1	A	A	183 - 273	183 - 273
3	X-RAY DIFFRACTION	2	B	B	1 - 98	1 - 98
4	X-RAY DIFFRACTION	3	C	C	1 - 9	1 - 9
5	X-RAY DIFFRACTION	4	D	D	2 - 182	2 - 182
6	X-RAY DIFFRACTION	4	D	D	183 - 273	183 - 273
7	X-RAY DIFFRACTION	5	E	E	1 - 98	1 - 98
8	X-RAY DIFFRACTION	6	F	F	1 - 9	1 - 9
9	X-RAY DIFFRACTION	7	G	G	2 - 182	2 - 182
10	X-RAY DIFFRACTION	7	G	G	183 - 273	183 - 273
11	X-RAY DIFFRACTION	8	H	H	1 - 98	1 - 98
12	X-RAY DIFFRACTION	9	I	I	1 - 9	1 - 9
13	X-RAY DIFFRACTION	10	J	J	2 - 182	2 - 182
14	X-RAY DIFFRACTION	10	J	J	183 - 273	183 - 273
15	X-RAY DIFFRACTION	11	K	K	1 - 98	1 - 98
16	X-RAY DIFFRACTION	12	L	L	1 - 9	1 - 9

Refinement

*PLUS

R_factor R_free: 0.279 / R_factor R_work: 0.241 / Lowest resolution: 20 Å

Solvent computation

*PLUS

Displacement parameters

*PLUS

Refine LS restraints

*PLUS

Refine-ID	Type	Dev ideal
X-RAY DIFFRACTION	r_bond_d	0.019
X-RAY DIFFRACTION	r_angle_d
X-RAY DIFFRACTION	r_angle_deg	1.92

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