PDB-8ag1: Crystal structure of a novel OX40 antibody

ID or keywords:

Entry

Database: PDB / ID: 8ag1

Title

Crystal structure of a novel OX40 antibody

Components

Novel OX40 antibody heavy chain
Novel OX40 antibody light chain
Tumor necrosis factor receptor superfamily member 4

Keywords

IMMUNE SYSTEM / OX40 / antibody / activation

Function / homology

Function and homology information

tumor necrosis factor receptor activity / TNFs bind their physiological receptors / positive regulation of immunoglobulin production / T cell proliferation / positive regulation of B cell proliferation / negative regulation of DNA-binding transcription factor activity / virus receptor activity / immune response / inflammatory response / external side of plasma membrane ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.303 Å

Authors

Gao, H. / Zhou, A.

Funding support

China, 1items

Citation

Journal: Biomolecules / Year: 2022
Title: Structural Basis of a Novel Agonistic Anti-OX40 Antibody.
Authors: Zhang, J. / Jiang, X. / Gao, H. / Zhang, F. / Zhang, X. / Zhou, A. / Xu, T. / Cai, H.

History

Deposition	Jul 19, 2022	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jul 19, 2023	Provider: repository / Type: Initial release
Revision 1.1	Feb 7, 2024	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2	Nov 6, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8ag1.cif.gz	545.7 KB	Display	PDBx/mmCIF format
PDB format	pdb8ag1.ent.gz	350.9 KB	Display	PDB format
PDBx/mmJSON format	8ag1.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	8ag1_validation.pdf.gz	476.2 KB	Display	wwPDB validaton report
Full document	8ag1_full_validation.pdf.gz	483.9 KB	Display
Data in XML	8ag1_validation.xml.gz	35.3 KB	Display
Data in CIF	8ag1_validation.cif.gz	48.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ag/8ag1 ftp://data.pdbj.org/pub/pdb/validation_reports/ag/8ag1	HTTPS FTP

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Related structure data

Related structure data	7yk4C 2ehy PDB Unreleased entryS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#21 - Sep 2001 Antibodies similarity (1) #256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1) #68 - Aug 2005 Neurotrophins similarity (5)

Deposited unit

L: Novel OX40 antibody light chain

H: Novel OX40 antibody heavy chain

h: Novel OX40 antibody heavy chain

l: Novel OX40 antibody light chain

A: Tumor necrosis factor receptor superfamily member 4

a: Tumor necrosis factor receptor superfamily member 4

hetero molecules

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

1

L: Novel OX40 antibody light chain

H: Novel OX40 antibody heavy chain

A: Tumor necrosis factor receptor superfamily member 4

hetero molecules

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

2

h: Novel OX40 antibody heavy chain

l: Novel OX40 antibody light chain

a: Tumor necrosis factor receptor superfamily member 4

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

Unit cell

Length a, b, c (Å)	162.356, 162.356, 232.145
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	180
Space group name H-M	P6₂22

#1: Antibody

Novel OX40 antibody light chain

Mass: 23610.170 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: Antibody

Novel OX40 antibody heavy chain

Mass: 26180.090 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Homo sapiens (human) / Cell line (production host): HEK293 / Production host:

Homo sapiens (human)

#3: Protein

Tumor necrosis factor receptor superfamily member 4 / ACT35 antigen / OX40L receptor / TAX transcriptionally-activated glycoprotein 1 receptor

Mass: 17027.002 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Homo sapiens (human) / Gene: TNFRSF4, TXGP1L / Production host:

Homo sapiens (human) / References: UniProt: P43489

#4: 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

#5: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 2 / 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: 3.3 Å³/Da / Density % sol: 62.78 %
Crystal grow	Temperature: 293 K / Method: evaporation / pH: 5 / Details: 0.1m CITRATE, PH5.6, 2% TACSIMATE, 16% PEG3350

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97853 Å
Detector	Type: DECTRIS PILATUS 12M / Detector: PIXEL / Date: Oct 1, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97853 Å / Relative weight: 1
Reflection	Resolution: 3.3→77.502 Å / Num. obs: 27927 / % possible obs: 99.7 % / Redundancy: 10.6 % / CC_1/2: 0.994 / R_merge(I) obs: 0.168 / Net I/σ(I): 9.1
Reflection shell	Resolution: 3.3→3.5 Å / R_merge(I) obs: 1.945 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 4370 / CC_1/2: 0.67

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Processing

Software

Name	Version	Classification
REFMAC	8.0.002	refinement
iMOSFLM		data reduction
SCALA		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2EHY

2ehy
PDB Unreleased entry

Resolution: 3.303→77.502 Å / Cor.coef. F_o:F_c: 0.873 / Cor.coef. F_o:F_c free: 0.856 / SU B: 47.584 / SU ML: 0.355 / Cross valid method: FREE R-VALUE / ESU R Free: 0.598
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2681	1132	5.084 %
R_work	0.1943	21133	-
all	0.198	-	-
obs	-	22265	80.148 %

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: 91.616 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-2.726 Å²	-1.363 Å²	-0 Å²
2-	-	-2.726 Å²	-0 Å²
3-	-	-	8.842 Å²

Refinement step

Cycle: LAST / Resolution: 3.303→77.502 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8016	0	14	2	8032

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.002	0.011	8258
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	7066
X-RAY DIFFRACTION	r_angle_refined_deg	0.593	1.644	11305
X-RAY DIFFRACTION	r_angle_other_deg	0.226	1.548	16577
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.873	5	1068
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	5.72	10	33
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	9.223	10	1201
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	9.566	10	320
X-RAY DIFFRACTION	r_chiral_restr	0.027	0.2	1277
X-RAY DIFFRACTION	r_gen_planes_refined	0.002	0.02	9416
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1577
X-RAY DIFFRACTION	r_nbd_refined	0.16	0.2	1529
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.162	0.2	7087
X-RAY DIFFRACTION	r_nbtor_refined	0.164	0.2	4118
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.079	0.2	4035
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.11	0.2	178
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.017	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.058	0.2	20
X-RAY DIFFRACTION	r_nbd_other	0.07	0.2	60
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.09	0.2	8
X-RAY DIFFRACTION	r_mcbond_it	5.523	9.802	4293
X-RAY DIFFRACTION	r_mcbond_other	5.523	9.802	4293
X-RAY DIFFRACTION	r_mcangle_it	8.38	14.687	5348
X-RAY DIFFRACTION	r_mcangle_other	8.38	14.688	5349
X-RAY DIFFRACTION	r_scbond_it	4.84	9.861	3965
X-RAY DIFFRACTION	r_scbond_other	4.839	9.862	3966
X-RAY DIFFRACTION	r_scangle_it	7.308	14.762	5955
X-RAY DIFFRACTION	r_scangle_other	7.308	14.762	5956
X-RAY DIFFRACTION	r_lrange_it	14.563	182.316	30712
X-RAY DIFFRACTION	r_lrange_other	14.564	182.32	30712
X-RAY DIFFRACTION	r_rigid_bond_restr	0.683	3	15324

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
3.303-3.389	0.316	14	0.189	267	0.195	2004	0.965	0.985	14.022	0.189
3.389-3.482	0.282	32	0.24	790	0.242	1941	0.953	0.966	42.3493	0.24
3.482-3.582	0.288	59	0.239	946	0.242	1899	0.947	0.966	52.9226	0.239
3.582-3.692	0.356	65	0.241	1114	0.247	1873	0.903	0.964	62.9471	0.241
3.692-3.813	0.328	67	0.234	1167	0.239	1780	0.928	0.965	69.3258	0.234
3.813-3.947	0.306	61	0.213	1296	0.218	1740	0.937	0.97	77.9885	0.213
3.947-4.095	0.264	85	0.193	1468	0.197	1691	0.952	0.977	91.8391	0.193
4.095-4.262	0.274	89	0.196	1535	0.2	1628	0.953	0.976	99.7543	0.196
4.262-4.451	0.279	75	0.193	1488	0.197	1564	0.952	0.976	99.9361	0.193
4.451-4.667	0.291	78	0.174	1413	0.18	1492	0.943	0.979	99.933	0.174
4.667-4.919	0.209	74	0.157	1366	0.16	1441	0.974	0.984	99.9306	0.157
4.919-5.216	0.221	75	0.145	1281	0.149	1356	0.968	0.987	100	0.145
5.216-5.574	0.248	68	0.147	1219	0.153	1287	0.96	0.984	100	0.147
5.574-6.018	0.241	49	0.177	1156	0.18	1205	0.963	0.979	100	0.177
6.018-6.589	0.328	44	0.176	1067	0.182	1113	0.96	0.978	99.8203	0.176
6.589-7.36	0.225	52	0.16	967	0.163	1019	0.963	0.983	100	0.16
7.36-8.486	0.174	42	0.15	868	0.151	910	0.983	0.986	100	0.15
8.486-10.362	0.162	35	0.148	755	0.149	790	0.984	0.986	100	0.148
10.362-14.524	0.289	45	0.215	588	0.22	633	0.923	0.966	100	0.215
14.524-77.502	0.498	23	0.484	382	0.485	410	0.843	0.767	98.7805	0.484

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	0.1575	0.0523	-0.437	0.3806	0.0066	2.4675	0.0445	0.0126	-0.0824	-0.0075	0.0747	-0.0815	-0.0035	0.1398	-0.1192	0.1243	0.019	-0.0064	0.3442	-0.0705	0.1654	222.9934	-47.9162	30.2886
2	0.4362	0.1134	0.7789	0.841	0.5401	2.2817	0.002	-0.1677	0.0508	-0.0715	0.0458	0.0416	-0.0825	-0.0637	-0.0479	0.1226	-0.0342	0.052	0.2253	0.0377	0.1673	206.1078	-43.6999	25.4957
3	1.036	0.1857	0.2755	2.0958	0.1608	1.5113	-0.057	0.0448	-0.1139	0.13	0.0993	-0.0062	0.1393	0.112	-0.0423	0.1166	0.0642	0.0504	0.1274	0.005	0.1189	206.308	-15.4542	7.9715
4	1.3407	0.6182	0.5817	1.6736	-0.0161	0.318	0.1051	-0.2465	-0.0116	0.2564	-0.0656	0.2105	-0.0102	-0.1534	-0.0395	0.1699	0.0058	0.0707	0.429	-0.0566	0.0749	197.4425	-3.3353	19.4245
5	1.5557	0.2447	0.3136	0.5289	0.0988	0.1073	-0.106	0.4293	0.0048	-0.4301	0.0961	-0.0724	0.0023	0.1219	0.0099	0.4808	-0.0366	0.0423	0.3808	0.0265	0.2212	224.6154	-49.9835	-13.4869
6	2.3191	-0.6396	-0.8261	3.3902	0.4472	0.3235	-0.4017	-0.1028	0.2655	0.6995	0.428	0.2755	0.1568	0.0972	-0.0263	0.3192	-0.0557	-0.0191	0.2153	0.0786	0.1995	171.8439	-28.9775	-0.2883

Refinement TLS group

Selection: ALL

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