PDB-8y74: Crystal structure of 9-mer peptide from H9N2 avian influenza viru...

ID or keywords:

Entry

Database: PDB / ID: 8y74

Title

Crystal structure of 9-mer peptide from H9N2 avian influenza virus in complex with BF2*0201

Components

Beta-2-microglobulin
MHC class I alpha chain 2
Polymerase basic protein 2

Keywords

IMMUNE SYSTEM / chicken MHC / 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 / cap snatching / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / antigen processing and presentation of peptide antigen via MHC class I / 7-methylguanosine mRNA capping / host cell mitochondrion ...
Similarity search - Function

Biological species

Gallus gallus (chicken)

Influenza A virus

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.9 Å

Authors

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

Funding support

China, 1items

Citation

Journal: J.Biol.Chem. / Year: 2024
Title: Revealing novel and conservative T-cell epitopes with MHC B2 restriction on H9N2 avian influenza virus (AIV).
Authors: Jia, Y. / Wu, Q. / Li, Y. / Ma, M. / Song, W. / Chen, R. / Yao, Y. / Nair, V. / Zhang, N. / Liao, M. / Dai, M.

History

Deposition	Feb 3, 2024	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Jul 10, 2024	Provider: repository / Type: Initial release
Revision 1.1	Nov 6, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 1.2	Jan 15, 2025	Group: Structure summary / Category: audit_author

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8y74.cif.gz	422.2 KB	Display	PDBx/mmCIF format
PDB format	pdb8y74.ent.gz	266.8 KB	Display	PDB format
PDBx/mmJSON format	8y74.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8y74_validation.pdf.gz	465.9 KB	Display	wwPDB validaton report
Full document	8y74_full_validation.pdf.gz	471.6 KB	Display
Data in XML	8y74_validation.xml.gz	34.9 KB	Display
Data in CIF	8y74_validation.cif.gz	46.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/y7/8y74 ftp://data.pdbj.org/pub/pdb/validation_reports/y7/8y74	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-00227 / 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

C: Polymerase basic protein 2

D: MHC class I alpha chain 2

E: Beta-2-microglobulin

F: Polymerase basic protein 2

87 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	125.782, 76.553, 87.143
Angle α, β, γ (deg.)	90.000, 92.449, 90.000
Int Tables number	5
Space group name H-M	C121

#1: Protein	MHC class I alpha chain 2 / MHC class I antigen / MHC class I glycoprotein / MHC class I molecule Mass: 31095.564 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: An extra methionine at the N-terminal of both the A and D chains is encoded by the starting codon ATG. Source: (gene. exp.) Gallus gallus (chicken) / Gene: BF2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O46789
#2: Protein	Beta-2-microglobulin Mass: 11193.601 Da / Num. of mol.: 2 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	Polymerase basic protein 2 / RNA-directed RNA polymerase subunit P3 Mass: 1217.395 Da / Num. of mol.: 2 / Source method: obtained synthetically Source: (synth.) Influenza A virus (A/chicken/Bangladesh/19495/2013(H9N2)) References: UniProt: A0A023PU38
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 251 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
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: 2.41 Å³/Da / Density % sol: 48.93 %
Crystal grow	Temperature: 291.15 K / Method: vapor diffusion, sitting drop Details: 0.1 M Imidazole pH 7.0, 20% w/v Polyethylene glycol 6,000

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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: 1.9→43.532 Å / Num. obs: 65173 / % possible obs: 100 % / Redundancy: 6.5 % / CC_1/2: 0.996 / Net I/σ(I): 9.1
Reflection shell	Resolution: 1.9→1.95 Å / Redundancy: 5.9 % / Mean I/σ(I) obs: 2 / Num. unique obs: 4776 / CC_1/2: 0.438 / % possible all: 100

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Processing

Software

Name	Version	Classification
xia2		data reduction
xia2		data scaling
PHASER		phasing
REFMAC	5.8.0425	refinement

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.9→43.532 Å / Cor.coef. F_o:F_c: 0.954 / Cor.coef. F_o:F_c free: 0.936 / WR_factor R_free: 0.252 / WR_factor R_work: 0.214 / SU B: 9.324 / SU ML: 0.12 / Average fsc free: 0.9581 / Average fsc work: 0.9694 / Cross valid method: FREE R-VALUE / ESU R: 0.164 / ESU R Free: 0.149
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2402	3321	5.097 %
R_work	0.2039	61831	-
all	0.206	-	-
obs	-	65152	99.951 %

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: 39.556 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.5 Å²	0 Å²	-0.321 Å²
2-	-	0.233 Å²	0 Å²
3-	-	-	0.293 Å²

Refinement step

Cycle: LAST / Resolution: 1.9→43.532 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6091	0	0	251	6342

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.012	6278
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	5608
X-RAY DIFFRACTION	r_angle_refined_deg	1.645	1.826	8538
X-RAY DIFFRACTION	r_angle_other_deg	0.592	1.774	12907
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.874	5	745
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	6.879	5	48
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.485	10	972
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	14.48	10	321
X-RAY DIFFRACTION	r_chiral_restr	0.086	0.2	857
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	7625
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1560
X-RAY DIFFRACTION	r_nbd_refined	0.208	0.2	1011
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.198	0.2	4954
X-RAY DIFFRACTION	r_nbtor_refined	0.183	0.2	2922
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.085	0.2	3148
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.149	0.2	245
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.111	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.104	0.2	10
X-RAY DIFFRACTION	r_nbd_other	0.11	0.2	78
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.18	0.2	27
X-RAY DIFFRACTION	r_mcbond_it	1.588	1.784	3007
X-RAY DIFFRACTION	r_mcbond_other	1.586	1.785	3007
X-RAY DIFFRACTION	r_mcangle_it	2.384	3.193	3743
X-RAY DIFFRACTION	r_mcangle_other	2.383	3.193	3744
X-RAY DIFFRACTION	r_scbond_it	2.394	2.082	3271
X-RAY DIFFRACTION	r_scbond_other	2.394	2.082	3272
X-RAY DIFFRACTION	r_scangle_it	3.687	3.687	4795
X-RAY DIFFRACTION	r_scangle_other	3.687	3.687	4796
X-RAY DIFFRACTION	r_lrange_it	4.911	17.855	6762
X-RAY DIFFRACTION	r_lrange_other	4.869	17.81	6730

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
1.9-1.949	0.31	249	0.284	4516	0.286	4767	0.925	0.935	99.958	0.261
1.949-2.003	0.283	222	0.242	4483	0.244	4707	0.95	0.964	99.9575	0.208
2.003-2.061	0.255	224	0.226	4270	0.227	4498	0.962	0.968	99.9111	0.196
2.061-2.124	0.263	196	0.223	4230	0.225	4427	0.96	0.969	99.9774	0.194
2.124-2.193	0.292	218	0.232	4059	0.236	4280	0.947	0.967	99.9299	0.202
2.193-2.27	0.244	217	0.223	3901	0.224	4127	0.961	0.959	99.7819	0.202
2.27-2.355	0.3	193	0.239	3803	0.242	3998	0.952	0.968	99.95	0.209
2.355-2.451	0.271	216	0.219	3642	0.222	3859	0.958	0.974	99.9741	0.195
2.451-2.56	0.251	221	0.215	3481	0.217	3702	0.961	0.974	100	0.198
2.56-2.684	0.309	170	0.222	3340	0.226	3510	0.947	0.972	100	0.211
2.684-2.829	0.277	194	0.22	3221	0.223	3415	0.952	0.971	100	0.217
2.829-3	0.248	156	0.21	3007	0.212	3163	0.961	0.974	100	0.214
3-3.206	0.229	127	0.213	2880	0.213	3007	0.969	0.974	100	0.225
3.206-3.461	0.223	163	0.211	2610	0.212	2773	0.97	0.979	100	0.223
3.461-3.789	0.226	138	0.202	2441	0.203	2579	0.974	0.98	100	0.223
3.789-4.233	0.231	118	0.17	2207	0.173	2325	0.973	0.985	100	0.202
4.233-4.88	0.192	92	0.141	2007	0.143	2100	0.981	0.989	99.9524	0.182
4.88-5.958	0.212	74	0.177	1669	0.178	1743	0.98	0.986	100	0.215
5.958-8.347	0.241	81	0.203	1310	0.205	1391	0.971	0.981	100	0.252
8.347-43.532	0.141	52	0.195	753	0.191	805	0.987	0.977	100	0.275

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	1.4175	0.6622	1.2851	0.9265	0.6001	2.9681	-0.0066	0.1213	0.0073	-0.071	0.0071	0.1204	0.2094	-0.1635	-0.0005	0.0652	0.0021	0.0127	0.0971	-0.0004	0.0663	-11.0965	5.2595	9.7474
2	1.8361	1.2688	0.3851	2.7094	1.4158	4.5257	0.0214	-0.0854	-0.0776	0.0581	-0.1265	0.2193	0.4312	-0.7273	0.1051	0.0711	-0.0484	-0.0065	0.1505	-0.0039	0.0462	-12.9844	5.3882	28.5479
3	4.1634	4.7041	0.0785	12.5542	-0.7855	2.1777	-0.0183	0.1914	0.1563	-0.3413	0.0592	0.5574	0.2097	-0.328	-0.0409	0.1474	-0.0032	-0.0312	0.2757	-0.0273	0.1842	-25.7565	0.1026	-2.8471
4	2.1153	-0.7641	0.5854	2.6179	0.3634	3.5377	-0.1521	-0.0631	0.1212	0.0395	-0.0391	-0.1894	-0.3878	-0.1848	0.1912	0.0497	0.0229	-0.0507	0.012	-0.0256	0.2289	-16.8026	-31.4442	40.2759
5	2.5541	-0.0635	1.3656	3.9444	1.5085	3.465	0.0505	0.0576	0.1389	-0.2554	-0.0481	0.0385	-0.1723	-0.2385	-0.0025	0.0903	0.043	-0.0073	0.1133	0.0285	0.1254	-27.8164	-32.286	24.9572
6	1.3702	-3.9902	-0.735	12.0444	2.4686	0.6817	-0.2796	-0.1793	0.0948	0.6752	0.2013	-0.0726	-0.0532	-0.139	0.0783	0.3796	0.1278	0.031	0.3338	-0.0758	0.2954	-23.698	-25.6557	58.5285
7	0.172	0.2231	-0.0405	0.3458	-0.0676	0.0183	-0.0309	0.0476	-0.0476	-0.0529	0.0485	0.0297	0.0214	-0.0331	-0.0176	0.1677	0.0288	-0.0182	0.2115	-0.0117	0.164	-11.5715	-6.3664	24.1307
8	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.158	0	0	0.158	0	0.158	0	0	0
9	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.158	0	0	0.158	0	0.158	0	0	0
10	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.158	0	0	0.158	0	0.158	0	0	0
11	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.158	0	0	0.158	0	0.158	0	0	0
12	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.158	0	0	0.158	0	0.158	0	0	0
13	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.158	0	0	0.158	0	0.158	0	0	0
14	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.158	0	0	0.158	0	0.158	0	0	0
15	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.158	0	0	0.158	0	0.158	0	0	0
16	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.158	0	0	0.158	0	0.158	0	0	0
17	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.158	0	0	0.158	0	0.158	0	0	0
18	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.158	0	0	0.158	0	0.158	0	0	0
19	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.158	0	0	0.158	0	0.158	0	0	0
20	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.158	0	0	0.158	0	0.158	0	0	0
21	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.158	0	0	0.158	0	0.158	0	0	0
22	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.158	0	0	0.158	0	0.158	0	0	0
23	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.158	0	0	0.158	0	0.158	0	0	0
24	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.158	0	0	0.158	0	0.158	0	0	0
25	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.158	0	0	0.158	0	0.158	0	0	0
26	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.158	0	0	0.158	0	0.158	0	0	0
27	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.158	0	0	0.158	0	0.158	0	0	0
28	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.158	0	0	0.158	0	0.158	0	0	0
29	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.158	0	0	0.158	0	0.158	0	0	0
30	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.158	0	0	0.158	0	0.158	0	0	0
31	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.158	0	0	0.158	0	0.158	0	0	0
32	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.158	0	0	0.158	0	0.158	0	0	0
33	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.158	0	0	0.158	0	0.158	0	0	0
34	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.158	0	0	0.158	0	0.158	0	0	0
35	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.158	0	0	0.158	0	0.158	0	0	0
36	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.158	0	0	0.158	0	0.158	0	0	0
37	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.158	0	0	0.158	0	0.158	0	0	0
38	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.158	0	0	0.158	0	0.158	0	0	0
39	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.158	0	0	0.158	0	0.158	0	0	0
40	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.158	0	0	0.158	0	0.158	0	0	0
41	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.158	0	0	0.158	0	0.158	0	0	0
42	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.158	0	0	0.158	0	0.158	0	0	0

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	A	0 - 271
2	X-RAY DIFFRACTION	8	ALL	A	0 - 271
3	X-RAY DIFFRACTION	15	ALL	A	0 - 271
4	X-RAY DIFFRACTION	22	ALL	A	0 - 271
5	X-RAY DIFFRACTION	29	ALL	A	0 - 271
6	X-RAY DIFFRACTION	36	ALL	A	0 - 271

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-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi