PDB-8z0h: Crystal structure of 9-mer peptide from ALV-J in complex with BF2*0201

ID or keywords:

Entry

Database: PDB / ID: 8z0h

Title

Crystal structure of 9-mer peptide from ALV-J in complex with BF2*0201

Components

Beta-2-microglobulin
Gag protein
MHC class I alpha chain 2

Keywords

IMMUNE SYSTEM / chicken MHC BF2*0201 T cell recognition

Function / homology

Function and homology information

ER-Phagosome pathway / Endosomal/Vacuolar pathway / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / DAP12 signaling / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / antigen processing and presentation of peptide antigen via MHC class I / viral process / Neutrophil degranulation / cellular response to iron ion / peptide antigen assembly with MHC class II protein complex ...
Similarity search - Function

Biological species

Gallus gallus (chicken)

Avian leukemia virus

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.72 Å

Authors

Jia, Y.S. / Ma, M.L. / Li, Y.L. / Liao, M. / Dai, M.M.

Funding support

China, 1items

Citation

Journal: Xu Mu Shou Yi Xue Bao / Year: 2024
Title: Structure and Mechanism of ALV-J Epitope Presented by MHC Class I Molecule BF20201
Authors: Jia, Y.S. / Li, Y.L. / Ma, M.L. / Liao, M. / Dai, M.M.

History

Deposition	Apr 9, 2024	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Jan 15, 2025	Provider: repository / Type: Initial release
Revision 1.1	Feb 5, 2025	Group: Database references / Category: citation Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.year

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8z0h.cif.gz	352.4 KB	Display	PDBx/mmCIF format
PDB format	pdb8z0h.ent.gz	273.1 KB	Display	PDB format
PDBx/mmJSON format	8z0h.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/z0/8z0h ftp://data.pdbj.org/pub/pdb/validation_reports/z0/8z0h	HTTPS FTP

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Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Experimental dataset #1	Data reference: 10.51093/xrd-00244 / Data set type: diffraction image data

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: MHC class I alpha chain 2

B: Beta-2-microglobulin

D: MHC class I alpha chain 2

E: Beta-2-microglobulin

G: MHC class I alpha chain 2

H: Beta-2-microglobulin

J: MHC class I alpha chain 2

K: Beta-2-microglobulin

I: Gag protein

C: Gag protein

F: Gag protein

L: Gag protein

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

1

A: MHC class I alpha chain 2

B: Beta-2-microglobulin

C: Gag protein

defined by author&software
Evidence: gel filtration
43.2 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

D: MHC class I alpha chain 2

E: Beta-2-microglobulin

F: Gag protein

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

3

G: MHC class I alpha chain 2

H: Beta-2-microglobulin

I: Gag protein

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

4

J: MHC class I alpha chain 2

K: Beta-2-microglobulin

L: Gag protein

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

Unit cell

Length a, b, c (Å)	86.614, 115.584, 94.107
Angle α, β, γ (deg.)	90.000, 111.158, 90.000
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Auth asym-ID: A / Label asym-ID: A

Dom-ID	Component-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth seq-ID	Label seq-ID
1	1	1	MET	MET	PRO	PRO	0 - 272	1 - 273
2	1	1	MET	MET	PRO	PRO	0 - 272	1 - 273
3	2	2	MET	MET	PRO	PRO	0 - 272	1 - 273
4	2	2	MET	MET	PRO	PRO	0 - 272	1 - 273
5	3	3	MET	MET	PRO	PRO	0 - 272	1 - 273
6	3	3	MET	MET	PRO	PRO	0 - 272	1 - 273
7	4	4	GLU	GLU	TYR	TYR	1 - 97	2 - 98
8	4	4	GLU	GLU	TYR	TYR	1 - 97	2 - 98
9	5	5	GLU	GLU	TYR	TYR	1 - 97	2 - 98
10	5	5	GLU	GLU	TYR	TYR	1 - 97	2 - 98
11	6	6	GLU	GLU	TYR	TYR	1 - 97	2 - 98
12	6	6	GLU	GLU	TYR	TYR	1 - 97	2 - 98
13	7	7	MET	MET	PRO	PRO	0 - 272	1 - 273
14	7	7	MET	MET	PRO	PRO	0 - 272	1 - 273
15	8	8	MET	MET	PRO	PRO	0 - 272	1 - 273
16	8	8	MET	MET	PRO	PRO	0 - 272	1 - 273
17	9	9	GLU	GLU	TYR	TYR	1 - 97	2 - 98
18	9	9	GLU	GLU	TYR	TYR	1 - 97	2 - 98
19	10	10	GLU	GLU	TYR	TYR	1 - 97	2 - 98
20	10	10	GLU	GLU	TYR	TYR	1 - 97	2 - 98
21	11	11	MET	MET	PRO	PRO	0 - 272	1 - 273
22	11	11	MET	MET	PRO	PRO	0 - 272	1 - 273
23	12	12	GLU	GLU	TYR	TYR	1 - 97	2 - 98
24	12	12	GLU	GLU	TYR	TYR	1 - 97	2 - 98

NCS ensembles :

ID	Details
1	Local NCS retraints between domains: 1 2
2	Local NCS retraints between domains: 3 4
3	Local NCS retraints between domains: 5 6
4	Local NCS retraints between domains: 7 8
5	Local NCS retraints between domains: 9 10
6	Local NCS retraints between domains: 11 12
7	Local NCS retraints between domains: 13 14
8	Local NCS retraints between domains: 15 16
9	Local NCS retraints between domains: 17 18
10	Local NCS retraints between domains: 19 20
11	Local NCS retraints between domains: 21 22
12	Local NCS retraints between domains: 23 24

#1: Protein	MHC class I alpha chain 2 / MHC class I antigen / MHC class I glycoprotein / MHC class I molecule Mass: 31192.678 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gallus gallus (chicken) / Gene: B-FIV, BF2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O46789
#2: Protein	Beta-2-microglobulin Mass: 10947.316 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gallus gallus (chicken) / Gene: B2M / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P21611
#3: Protein/peptide	Gag protein Mass: 1021.147 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Avian leukemia virus / References: UniProt: G0Z7Q1
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1440 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.54 Å³/Da / Density % sol: 51.66 %
Crystal grow	Temperature: 291.15 K / Method: vapor diffusion, sitting drop Details: 1.0 M Succinic acid pH 7.0, 0.1 M HEPES pH 7.0, 1% w/v Polyethylene glycol monomethyl ether 2,000

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.979183 Å
Detector	Type: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Aug 22, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979183 Å / Relative weight: 1
Reflection	Resolution: 1.72→115.58 Å / Num. obs: 180693 / % possible obs: 98.9 % / Redundancy: 3.3 % / CC_1/2: 0.993 / Net I/σ(I): 11.2
Reflection shell	Resolution: 1.72→1.76 Å / Mean I/σ(I) obs: 2.3 / Num. unique obs: 13135 / CC_1/2: 0.507

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Processing

Software

Name	Version	Classification
DIALS		data reduction
DIALS		data scaling
PHASER		phasing
REFMAC	5.8.0425	refinement

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.72→87.763 Å / Cor.coef. F_o:F_c: 0.956 / Cor.coef. F_o:F_c free: 0.939 / SU B: 2.287 / SU ML: 0.073 / Cross valid method: FREE R-VALUE / ESU R: 0.109 / ESU R Free: 0.105
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2123	8875	4.917 %
R_work	0.1821	171627	-
all	0.184	-	-
obs	-	180502	98.721 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 18.963 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.001 Å²	-0 Å²	-0.001 Å²
2-	-	-0.002 Å²	-0 Å²
3-	-	-	0.003 Å²

Refinement step

Cycle: LAST / Resolution: 1.72→87.763 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	12179	0	0	1440	13619

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.012	12551
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	11204
X-RAY DIFFRACTION	r_angle_refined_deg	1.511	1.677	17070
X-RAY DIFFRACTION	r_angle_other_deg	0.527	1.587	25804
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.76	5	1504
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	6.881	5	96
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.675	10	1940
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	17.58	10	640
X-RAY DIFFRACTION	r_chiral_restr	0.078	0.2	1712
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.02	15276
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	3104
X-RAY DIFFRACTION	r_nbd_refined	0.207	0.2	2117
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.191	0.2	10015
X-RAY DIFFRACTION	r_nbtor_refined	0.183	0.2	5978
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.084	0.2	6522
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.167	0.2	1090
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.178	0.2	3
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.308	0.2	22
X-RAY DIFFRACTION	r_nbd_other	0.182	0.2	110
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.184	0.2	65
X-RAY DIFFRACTION	r_mcbond_it	2.129	1.844	6052
X-RAY DIFFRACTION	r_mcbond_other	2.129	1.844	6052
X-RAY DIFFRACTION	r_mcangle_it	3.156	3.301	7544
X-RAY DIFFRACTION	r_mcangle_other	3.156	3.301	7545
X-RAY DIFFRACTION	r_scbond_it	3.22	2.191	6499
X-RAY DIFFRACTION	r_scbond_other	3.219	2.191	6500
X-RAY DIFFRACTION	r_scangle_it	5.084	3.836	9526
X-RAY DIFFRACTION	r_scangle_other	5.084	3.836	9527
X-RAY DIFFRACTION	r_lrange_it	7.041	22.642	14287
X-RAY DIFFRACTION	r_lrange_other	6.961	20.909	13892
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.098	0.05	8787
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.089	0.05	8851
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.094	0.05	8763
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.085	0.05	2889
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.082	0.05	2904
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.098	0.05	2886
X-RAY DIFFRACTION	r_ncsr_local_group_7	0.099	0.05	8802
X-RAY DIFFRACTION	r_ncsr_local_group_8	0.098	0.05	8810
X-RAY DIFFRACTION	r_ncsr_local_group_9	0.083	0.05	2926
X-RAY DIFFRACTION	r_ncsr_local_group_10	0.086	0.05	2943
X-RAY DIFFRACTION	r_ncsr_local_group_11	0.095	0.05	8801
X-RAY DIFFRACTION	r_ncsr_local_group_12	0.084	0.05	2946

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	A	X-RAY DIFFRACTION	Local ncs	0.0983	0.05009
1	2	A	X-RAY DIFFRACTION	Local ncs	0.0983	0.05009
2	3	A	X-RAY DIFFRACTION	Local ncs	0.08947	0.05009
2	4	A	X-RAY DIFFRACTION	Local ncs	0.08947	0.05009
3	5	A	X-RAY DIFFRACTION	Local ncs	0.09385	0.05009
3	6	A	X-RAY DIFFRACTION	Local ncs	0.09385	0.05009
4	7	A	X-RAY DIFFRACTION	Local ncs	0.08533	0.0501
4	8	A	X-RAY DIFFRACTION	Local ncs	0.08533	0.0501
5	9	A	X-RAY DIFFRACTION	Local ncs	0.08181	0.0501
5	10	A	X-RAY DIFFRACTION	Local ncs	0.08181	0.0501
6	11	A	X-RAY DIFFRACTION	Local ncs	0.0977	0.0501
6	12	A	X-RAY DIFFRACTION	Local ncs	0.0977	0.0501
7	13	A	X-RAY DIFFRACTION	Local ncs	0.09884	0.05009
7	14	A	X-RAY DIFFRACTION	Local ncs	0.09884	0.05009
8	15	A	X-RAY DIFFRACTION	Local ncs	0.0983	0.05009
8	16	A	X-RAY DIFFRACTION	Local ncs	0.0983	0.05009
9	17	A	X-RAY DIFFRACTION	Local ncs	0.08293	0.0501
9	18	A	X-RAY DIFFRACTION	Local ncs	0.08293	0.0501
10	19	A	X-RAY DIFFRACTION	Local ncs	0.08589	0.0501
10	20	A	X-RAY DIFFRACTION	Local ncs	0.08589	0.0501
11	21	A	X-RAY DIFFRACTION	Local ncs	0.09505	0.05009
11	22	A	X-RAY DIFFRACTION	Local ncs	0.09505	0.05009
12	23	A	X-RAY DIFFRACTION	Local ncs	0.08371	0.05011
12	24	A	X-RAY DIFFRACTION	Local ncs	0.08371	0.05011

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
1.72-1.765	0.28	618	0.254	12485	0.255	13518	0.949	0.956	96.93	0.221
1.765-1.813	0.261	631	0.236	12185	0.237	13103	0.957	0.965	97.8097	0.202
1.813-1.866	0.268	578	0.225	11929	0.227	12778	0.957	0.967	97.8792	0.192
1.866-1.923	0.232	582	0.205	11630	0.207	12445	0.965	0.973	98.1278	0.175
1.923-1.986	0.237	616	0.202	11203	0.204	12012	0.96	0.974	98.3933	0.176
1.986-2.056	0.236	595	0.196	10885	0.198	11666	0.963	0.974	98.4056	0.173
2.056-2.133	0.225	528	0.195	10555	0.196	11231	0.965	0.976	98.6822	0.176
2.133-2.22	0.217	534	0.186	10168	0.188	10840	0.972	0.978	98.7269	0.17
2.22-2.319	0.213	511	0.188	9708	0.19	10326	0.969	0.975	98.9638	0.169
2.319-2.432	0.229	517	0.192	9325	0.194	9936	0.967	0.976	99.0539	0.175
2.432-2.563	0.223	447	0.177	8935	0.179	9453	0.971	0.98	99.2489	0.164
2.563-2.719	0.211	461	0.18	8438	0.182	8956	0.972	0.979	99.3636	0.171
2.719-2.906	0.214	403	0.179	7948	0.181	8397	0.969	0.98	99.4522	0.174
2.906-3.139	0.196	372	0.173	7405	0.174	7810	0.975	0.981	99.5775	0.173
3.139-3.438	0.2	361	0.173	6831	0.175	7215	0.976	0.984	99.6812	0.178
3.438-3.843	0.178	331	0.162	6195	0.163	6541	0.983	0.986	99.7707	0.17
3.843-4.436	0.177	274	0.143	5488	0.145	5768	0.984	0.988	99.896	0.157
4.436-5.43	0.172	222	0.142	4662	0.144	4884	0.988	0.99	100	0.157
5.43-7.664	0.218	193	0.204	3620	0.204	3814	0.98	0.985	99.9738	0.216
7.664-87.763	0.218	101	0.18	2032	0.182	2147	0.981	0.983	99.3479	0.2

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