PDB-7nzh: Crystal structure of HLA-DR4 in complex with a citrullinated cilp...

ID or keywords:

Entry

Database: PDB / ID: 7nzh

Title

Crystal structure of HLA-DR4 in complex with a citrullinated cilp peptide

Components

HLA class II histocompatibility antigen, DR alpha chain
HLA class II histocompatibility antigen, DR beta chain
citrullinated cartilage intermediate layer protein (CILP) peptide 982-996

Keywords

IMMUNE SYSTEM / Complex / MHCII

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.831 Å

Authors

Ge, C. / Holmdahl, R.

Funding support

Sweden, 3items

Citation

Journal: Ann Rheum Dis / Year: 2022
Title: Key interactions in the trimolecular complex consisting of the rheumatoid arthritis-associated DRB1*04:01 molecule, the major glycosylated collagen II peptide and the T-cell receptor.
Authors: Ge, C. / Weisse, S. / Xu, B. / Dobritzsch, D. / Viljanen, J. / Kihlberg, J. / Do, N.N. / Schneider, N. / Lanig, H. / Holmdahl, R. / Burkhardt, H.

History

Deposition	Mar 24, 2021	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	May 11, 2022	Provider: repository / Type: Initial release
Revision 2.0	Nov 15, 2023	Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Refinement description Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / atom_type / chem_comp_atom / chem_comp_bond / pdbx_validate_close_contact / pdbx_validate_main_chain_plane / pdbx_validate_peptide_omega / pdbx_validate_rmsd_angle / pdbx_validate_torsion / struct_conn / struct_ncs_dom_lim Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site.occupancy / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_atom_id_2 / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 2.1	Jan 31, 2024	Group: Refinement description / Category: pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	7nzh.cif.gz	589.1 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	7nzh_validation.pdf.gz	1.2 MB	Display	wwPDB validaton report
Full document	7nzh_full_validation.pdf.gz	1.2 MB	Display
Data in XML	7nzh_validation.xml.gz	31.3 KB	Display
Data in CIF	7nzh_validation.cif.gz	41.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/nz/7nzh ftp://data.pdbj.org/pub/pdb/validation_reports/nz/7nzh	HTTPS FTP

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Related structure data

Related structure data	7nzeC 7nzfC 7o00C 6bilS S: Starting model for refinement C: citing same article (ref.)

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

AAA: HLA class II histocompatibility antigen, DR alpha chain

BBB: HLA class II histocompatibility antigen, DR beta chain

CCC: HLA class II histocompatibility antigen, DR alpha chain

DDD: HLA class II histocompatibility antigen, DR beta chain

EEE: citrullinated cartilage intermediate layer protein (CILP) peptide 982-996

FFF: citrullinated cartilage intermediate layer protein (CILP) peptide 982-996

hetero molecules

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

1

Idetical with deposited unit
defined by author
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	97.277, 112.244, 212.981
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	20
Space group name H-M	C222₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	AAA
2	1	CCC
3	2	BBB
4	2	DDD

NCS domain segments:

Component-ID: _

Dom-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	GLU	GLU	GLU	GLU	AAA	A	4 - 179	3 - 178
2	1	GLU	GLU	GLU	GLU	CCC	C	4 - 179	3 - 178
3	2	ASP	ASP	ALA	ALA	BBB	B	2 - 190	1 - 189
4	2	ASP	ASP	ALA	ALA	DDD	D	2 - 190	1 - 189

NCS ensembles :

ID	Details
1	Local NCS retraints between domains: 1 2
2	Local NCS retraints between domains: 3 4

#1: Protein

HLA class II histocompatibility antigen, DR alpha chain

Mass: 20971.670 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Homo sapiens (human) / Production host:

Homo sapiens (human)

#2: Protein

HLA class II histocompatibility antigen, DR beta chain

Mass: 22218.697 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Homo sapiens (human) / Production host:

Homo sapiens (human)

#3: Protein/peptide

citrullinated cartilage intermediate layer protein (CILP) peptide 982-996

Mass: 1639.811 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.)

Homo sapiens (human)

#4: Polysaccharide

2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source

Descriptor	Type	Program
DGlcpNAcb1-4DGlcpNAcb1-ROH	Glycam Condensed Sequence	GMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1	WURCS	PDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][a-D-GlcpNAc]{}}	LINUCS	PDB-CARE

#5: Sugar

ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE

Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₈H₁₅NO₆

Identifier	Type	Program
DGlcpNAcb	CONDENSED IUPAC CARBOHYDRATE SYMBOL	GMML 1.0
N-acetyl-b-D-glucopyranosamine	COMMON NAME	GMML 1.0
b-D-GlcpNAc	IUPAC CARBOHYDRATE SYMBOL	PDB-CARE 1.0
GlcNAc	SNFG CARBOHYDRATE SYMBOL	GMML 1.0

Has ligand of interest

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: 3.24 Å³/Da / Density % sol: 62.06 %
Crystal grow	Temperature: 290 K / Method: evaporation Details: 0.1M sodium acetate trihydrate pH 5.5, 0.2M lithium chloride, 18% (w/v) PEG6000

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

ESRF

/ Beamline: ID23-1 / Wavelength: 0.9763 Å

Detector

Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 16, 2016

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.9763 Å / Relative weight: 1

Reflection

Resolution: 2.83→56.12 Å / Num. obs: 27807 / % possible obs: 98.6 % / Redundancy: 13.3 % / CC_1/2: 0.998 / R_merge(I) obs: 0.151 / R_pim(I) all: 0.061 / R_rim(I) all: 0.164 / Net I/σ(I): 14.4

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all
8.95-56.12	11.5	0.042	3932	0.999	0.017	0.045
2.83-2.98	13.2	1.617	971	0.612	0.659	1.749

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
XDS		data reduction
XDS		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6BIL

6bil

Resolution: 2.831→49.698 Å / Cor.coef. F_o:F_c: 0.917 / Cor.coef. F_o:F_c free: 0.884 / SU B: 43.645 / SU ML: 0.363 / Cross valid method: FREE R-VALUE / ESU R: 2.03 / ESU R Free: 0.404
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2833	1402	5.051 %
R_work	0.2445	26354	-
all	0.246	-	-
obs	-	27756	98.457 %

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: 89.442 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.283 Å²	-0 Å²	-0 Å²
2-	-	-1.032 Å²	-0 Å²
3-	-	-	1.315 Å²

Refinement step

Cycle: LAST / Resolution: 2.831→49.698 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6252	0	142	0	6394

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.013	6587
X-RAY DIFFRACTION	r_bond_other_d	0.011	0.017	5951
X-RAY DIFFRACTION	r_ext_dist_refined_d	0.312	0.1	93603
X-RAY DIFFRACTION	r_angle_refined_deg	1.622	1.683	8936
X-RAY DIFFRACTION	r_angle_other_deg	1.381	1.608	13696
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	9.232	5	748
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	32.111	21.88	399
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.653	15	1028
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.103	15	50
X-RAY DIFFRACTION	r_chiral_restr	0.071	0.2	826
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	7377
X-RAY DIFFRACTION	r_gen_planes_other	0.009	0.02	1638
X-RAY DIFFRACTION	r_nbd_refined	0.223	0.2	1110
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.192	0.2	5579
X-RAY DIFFRACTION	r_nbtor_refined	0.171	0.2	3052
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.089	0.2	3539
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.226	0.2	87
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.509	0.2	2
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.421	0.2	22
X-RAY DIFFRACTION	r_nbd_other	0.228	0.2	27
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.202	0.2	4
X-RAY DIFFRACTION	r_mcbond_it	2.089	4.878	3022
X-RAY DIFFRACTION	r_mcbond_other	2.085	4.877	3021
X-RAY DIFFRACTION	r_mcangle_it	3.389	7.31	3760
X-RAY DIFFRACTION	r_mcangle_other	3.389	7.31	3761
X-RAY DIFFRACTION	r_scbond_it	2.623	5.278	3564
X-RAY DIFFRACTION	r_scbond_other	2.623	5.278	3564
X-RAY DIFFRACTION	r_scangle_it	4.376	7.791	5175
X-RAY DIFFRACTION	r_scangle_other	4.376	7.791	5176
X-RAY DIFFRACTION	r_lrange_it	9.21	189.986	94364
X-RAY DIFFRACTION	r_lrange_other	9.21	189.985	94365
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.082	0.05	5548
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.096	0.05	5865

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	AAA	X-RAY DIFFRACTION	Local ncs	0.08191	0.05009
1	2	CCC	X-RAY DIFFRACTION	Local ncs	0.08191	0.05009
2	3	BBB	X-RAY DIFFRACTION	Local ncs	0.09566	0.0501
2	4	DDD	X-RAY DIFFRACTION	Local ncs	0.09566	0.0501

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.831-2.905	0.38	105	0.378	1839	X-RAY DIFFRACTION	95.5752
2.905-2.984	0.39	92	0.332	1900	X-RAY DIFFRACTION	98.3218
2.984-3.071	0.35	90	0.314	1821	X-RAY DIFFRACTION	98.1006
3.071-3.165	0.335	89	0.3	1766	X-RAY DIFFRACTION	98.4607
3.165-3.269	0.301	82	0.269	1741	X-RAY DIFFRACTION	98.222
3.269-3.383	0.303	93	0.263	1670	X-RAY DIFFRACTION	98.657
3.383-3.511	0.31	74	0.263	1622	X-RAY DIFFRACTION	98.6047
3.511-3.654	0.286	93	0.252	1534	X-RAY DIFFRACTION	99.1469
3.654-3.816	0.232	89	0.232	1491	X-RAY DIFFRACTION	98.8736
3.816-4.002	0.316	77	0.238	1446	X-RAY DIFFRACTION	99.2182
4.002-4.219	0.315	72	0.222	1347	X-RAY DIFFRACTION	98.6101
4.219-4.474	0.212	77	0.194	1292	X-RAY DIFFRACTION	98.8448
4.474-4.782	0.189	59	0.178	1218	X-RAY DIFFRACTION	99.5323
4.782-5.165	0.2	63	0.2	1149	X-RAY DIFFRACTION	98.8581
5.165-5.656	0.28	65	0.221	1069	X-RAY DIFFRACTION	99.3865
5.656-6.322	0.314	59	0.246	938	X-RAY DIFFRACTION	98.4205
6.322-7.295	0.361	38	0.287	863	X-RAY DIFFRACTION	99.3385
7.295-8.925	0.292	31	0.251	741	X-RAY DIFFRACTION	99.6129
8.925-12.577	0.297	37	0.229	574	X-RAY DIFFRACTION	97.4482
12.577-49.698	0.388	17	0.348	333	X-RAY DIFFRACTION	95.6284

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	4.505	-1.4502	-1.2561	2.0933	1.1801	2.3441	-0.197	-0.2391	0.2227	0.2381	0.2233	-0.2297	-0.1558	0.1485	-0.0262	0.0868	0.0202	-0.0829	0.0281	-0.0035	0.2454	-21.9636	-14.5621	12.3629
2	2.792	-2.1157	-0.4473	3.6437	0.7544	1.5517	-0.242	-0.1732	-0.4291	0.4798	0.2048	0.2533	0.2582	-0.0441	0.0372	0.0859	0.0145	0.0499	0.023	0.0194	0.2391	-30.046	-29.9601	14.069
3	4.7118	-2.3572	-1.4375	2.7025	1.3429	3.7133	-0.2098	-0.5504	-0.3598	0.8591	0.2334	-0.0598	0.7411	0.1531	-0.0236	1.1932	0.2558	-0.1408	0.3185	0.0199	0.3729	-19.0244	-33.0014	39.4061
4	4.203	-0.3228	-1.742	1.0824	0.3477	2.8956	-0.1222	-0.5544	0.428	0.832	0.4062	-0.3301	0.0757	0.4433	-0.284	0.8327	0.3015	-0.307	0.3709	-0.1967	0.5305	-12.4563	-16.9592	37.4073
5	0.9775	-1.388	-2.7033	10.7089	12.1177	16.2469	0.0427	-0.1917	0.1816	-0.3055	-0.1269	0.3656	-0.8283	0.1385	0.0842	0.2807	0.0195	-0.0872	0.2057	0.0168	0.418	-44.4415	-7.1529	13.2603
6	20.4295	-0.737	5.0719	0.6915	-0.2935	1.2855	0.0884	-0.475	-1.2119	0.1732	0.2205	-0.0029	-0.0637	-0.1709	-0.3089	0.5043	0.035	0.0625	0.6989	-0.0544	0.3676	-32.1571	-20.9002	55.8163

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	AAA	2 - 181
2	X-RAY DIFFRACTION	1	ALL	AaA	182
3	X-RAY DIFFRACTION	1	ALL	AbA	183
4	X-RAY DIFFRACTION	2	ALL	BBB	2 - 190
5	X-RAY DIFFRACTION	2	ALL	BaB	191
6	X-RAY DIFFRACTION	3	ALL	CCC	4 - 180
7	X-RAY DIFFRACTION	3	ALL	CaC	183
8	X-RAY DIFFRACTION	4	ALL	DDD	2 - 190
9	X-RAY DIFFRACTION	5	ALL	EEE	1 - 14
10	X-RAY DIFFRACTION	5	ALL	EaE	7
11	X-RAY DIFFRACTION	6	ALL	FFF	1168 - 1180
12	X-RAY DIFFRACTION	6	ALL	FaF	1174

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