PDB-8oz3: Crystal structure of scFv ATOR 1017 bound to human 4-1BB

ID or keywords:

Entry

Database: PDB / ID: 8oz3

Title

Crystal structure of scFv ATOR 1017 bound to human 4-1BB

Components

(Single chain Fv) x 2
Tumor necrosis factor receptor superfamily member 9

Keywords

IMMUNE SYSTEM / complex / single chain Fv / tumor necrosis factor

Function / homology

Function and homology information

TNFs bind their physiological receptors / regulation of immature T cell proliferation in thymus / signaling receptor activity / regulation of cell population proliferation / negative regulation of cell population proliferation / external side of plasma membrane / apoptotic process / plasma membrane
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.1 Å

Authors

Hakansson, M. / Von Schantz, L. / Rose, N.

Funding support

1items

Citation

Journal: Cancer Immunol.Immunother. / Year: 2023
Title: ATOR-1017 (evunzekibart), an Fc-gamma receptor conditional 4-1BB agonist designed for optimal safety and efficacy, activates exhausted T cells in combination with anti-PD-1.
Authors: Enell Smith, K. / Fritzell, S. / Nilsson, A. / Barchan, K. / Rosen, A. / Schultz, L. / Varas, L. / Sall, A. / Rose, N. / Hakansson, M. / von Schantz, L. / Ellmark, P.

History

Deposition	May 8, 2023	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Mar 13, 2024	Provider: repository / Type: Initial release
Revision 1.1	Nov 6, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8oz3.cif.gz	697.3 KB	Display	PDBx/mmCIF format
PDB format	pdb8oz3.ent.gz	452.1 KB	Display	PDB format
PDBx/mmJSON format	8oz3.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	8oz3_validation.pdf.gz	473.3 KB	Display	wwPDB validaton report
Full document	8oz3_full_validation.pdf.gz	485.7 KB	Display
Data in XML	8oz3_validation.xml.gz	26.8 KB	Display
Data in CIF	8oz3_validation.cif.gz	36.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/oz/8oz3 ftp://data.pdbj.org/pub/pdb/validation_reports/oz/8oz3	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

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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) #126 - Jun 2010 Epidermal Growth Factor similarity (1) #182 - Feb 2015 Insulin receptor similarity (1) #184 - Apr 2015 Glucagon similarity (1)

Deposited unit

A: Single chain Fv

B: Single chain Fv

C: Tumor necrosis factor receptor superfamily member 9

D: Tumor necrosis factor receptor superfamily member 9

H: Single chain Fv

L: Single chain Fv

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

1

A: Single chain Fv

B: Single chain Fv

C: Tumor necrosis factor receptor superfamily member 9

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

2

D: Tumor necrosis factor receptor superfamily member 9

H: Single chain Fv

L: Single chain Fv

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

Unit cell

Length a, b, c (Å)	61.923, 125.214, 128.785
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	18
Space group name H-M	P22₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	A
3	2	A
4	2	A
5	3	A
6	3	A

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Auth asym-ID	Auth seq-ID
1	1	1	A	2 - 117
2	1	1	A	2 - 117
3	2	2	A	2 - 110
4	2	2	A	2 - 110
5	3	3	A	26 - 161
6	3	3	A	26 - 161

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

#1: Antibody	Single chain Fv Mass: 24449.285 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	Single chain Fv Mass: 23603.170 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Protein	Tumor necrosis factor receptor superfamily member 9 / 4-1BB ligand receptor / CDw137 / T-cell antigen 4-1BB homolog / T-cell antigen ILA Mass: 15118.044 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TNFRSF9, CD137, ILA / Production host: Homo sapiens (human) / References: UniProt: Q07011
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 10 / 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: 2.18 Å³/Da / Density % sol: 43.47 %
Crystal grow	Temperature: 293 K / Method: evaporation Details: 1.1 M sodium/potassium tartrate and 0.1 M MES pH 6.5

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.992 Å
Detector	Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 26, 2023
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.992 Å / Relative weight: 1
Reflection	Resolution: 3.1→89.8 Å / Num. obs: 18851 / % possible obs: 100 % / Redundancy: 11.7 % / CC_1/2: 0.997 / Net I/σ(I): 7.5
Reflection shell	Resolution: 3.1→3.31 Å / Num. unique obs: 3345 / CC_1/2: 1

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0405	refinement
autoXDS		data reduction
autoXDS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 3.1→89.776 Å / Cor.coef. F_o:F_c: 0.956 / Cor.coef. F_o:F_c free: 0.885 / WR_factor R_free: 0.312 / WR_factor R_work: 0.201 / SU B: 66.285 / SU ML: 0.456 / Average fsc free: 0.9089 / Average fsc work: 0.9377 / Cross valid method: THROUGHOUT / ESU R Free: 0.472
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2708	915	4.865 %	RANDOM
R_work	0.2047	17894	-	-
all	0.208	-	-	-
obs	-	18809	99.942 %	-

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: 130.402 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-11.3 Å²	0 Å²	-0 Å²
2-	-	13.769 Å²	-0 Å²
3-	-	-	-2.469 Å²

Refinement step

Cycle: LAST / Resolution: 3.1→89.776 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5463	0	0	10	5473

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.006	0.011	5601
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	4998
X-RAY DIFFRACTION	r_angle_refined_deg	1.332	1.646	7586
X-RAY DIFFRACTION	r_angle_other_deg	0.461	1.568	11579
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.666	5	719
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	16.62	5	34
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.416	10	902
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	17.181	10	235
X-RAY DIFFRACTION	r_chiral_restr	0.061	0.2	805
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	6669
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1335
X-RAY DIFFRACTION	r_nbd_refined	0.21	0.2	854
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.217	0.2	4683
X-RAY DIFFRACTION	r_nbtor_refined	0.176	0.2	2693
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.084	0.2	3080
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.203	0.2	96
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.137	0.2	2
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.222	0.2	12
X-RAY DIFFRACTION	r_nbd_other	0.18	0.2	63
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.142	0.2	3
X-RAY DIFFRACTION	r_mcbond_it	9.145	9.689	2894
X-RAY DIFFRACTION	r_mcbond_other	9.144	9.689	2894
X-RAY DIFFRACTION	r_mcangle_it	13.319	17.448	3607
X-RAY DIFFRACTION	r_mcangle_other	13.317	17.447	3608
X-RAY DIFFRACTION	r_scbond_it	10.502	10.348	2707
X-RAY DIFFRACTION	r_scbond_other	10.5	10.348	2708
X-RAY DIFFRACTION	r_scangle_it	15.127	18.803	3979
X-RAY DIFFRACTION	r_scangle_other	15.126	18.801	3980
X-RAY DIFFRACTION	r_lrange_it	18.577	120.773	22311
X-RAY DIFFRACTION	r_lrange_other	18.577	120.771	22312
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.085	0.05	3557
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.139	0.05	3254
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.159	0.05	3708

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	0.08524	0.0501
1	2	A	X-RAY DIFFRACTION	Local ncs	0.08524	0.0501
2	3	A	X-RAY DIFFRACTION	Local ncs	0.13892	0.05009
2	4	A	X-RAY DIFFRACTION	Local ncs	0.13892	0.05009
3	5	A	X-RAY DIFFRACTION	Local ncs	0.15905	0.05009
3	6	A	X-RAY DIFFRACTION	Local ncs	0.15905	0.05009

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
3.1-3.18	0.445	64	0.405	1274	0.407	1338	0.788	0.851	100	0.411
3.18-3.267	0.466	51	0.374	1292	0.378	1343	0.747	0.854	100	0.369
3.267-3.362	0.379	51	0.359	1214	0.359	1265	0.832	0.853	100	0.349
3.362-3.465	0.312	76	0.342	1206	0.34	1283	0.873	0.868	99.9221	0.335
3.465-3.579	0.373	64	0.285	1175	0.289	1239	0.853	0.914	100	0.276
3.579-3.704	0.321	69	0.27	1089	0.273	1159	0.903	0.933	99.9137	0.263
3.704-3.844	0.258	56	0.203	1100	0.206	1157	0.946	0.966	99.9136	0.191
3.844-4	0.237	45	0.19	1052	0.191	1099	0.961	0.976	99.818	0.18
4-4.178	0.229	59	0.169	1011	0.173	1070	0.971	0.98	100	0.163
4.178-4.381	0.215	38	0.167	972	0.169	1012	0.964	0.981	99.8024	0.16
4.381-4.618	0.201	58	0.152	918	0.155	976	0.971	0.984	100	0.147
4.618-4.897	0.179	43	0.132	867	0.135	911	0.977	0.987	99.8902	0.128
4.897-5.234	0.19	28	0.142	847	0.144	875	0.973	0.987	100	0.141
5.234-5.652	0.266	43	0.179	775	0.183	819	0.951	0.979	99.8779	0.179
5.652-6.189	0.196	33	0.17	720	0.172	753	0.968	0.984	100	0.17
6.189-6.915	0.266	26	0.196	658	0.199	684	0.96	0.978	100	0.199
6.915-7.977	0.286	29	0.191	589	0.195	618	0.953	0.974	100	0.195
7.977-9.751	0.226	27	0.17	495	0.172	522	0.967	0.982	100	0.185
9.751-13.709	0.208	32	0.206	398	0.206	430	0.975	0.982	100	0.219
13.709-89.776	0.523	23	0.288	242	0.308	267	0.822	0.945	99.2509	0.395

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	6.0783	0.1218	1.0203	4.996	-2.785	2.8389	-0.3979	-0.2685	0.8952	0.0315	0.2119	0.1539	-0.7005	0.1915	0.1861	0.4793	-0.1785	0.0513	0.1859	-0.0819	0.5249	-37.4152	-16.6811	-10.3733
2	6.379	1.6863	-0.8005	3.4216	-1.892	2.4194	0.1062	-1.153	-0.5711	0.3912	-0.0416	0.0907	0.0531	-0.3545	-0.0646	0.1478	-0.1144	0.0486	0.53	-0.0301	0.2376	-39.9286	-35.4257	1.688
3	1.464	-1.1834	-3.0265	1.4628	2.7168	7.2394	-0.0796	0.0392	-0.2601	-0.042	-0.1667	0.1317	-0.0605	0.0047	0.2462	0.138	-0.091	-0.0364	0.2766	0.0235	0.3241	-20.9362	-27.2217	14.6097
4	1.3914	-2.4154	1.1367	6.931	-3.731	2.068	-0.1905	-0.1006	0.1458	0.173	0.0988	-0.1778	-0.0968	-0.0386	0.0916	0.2704	-0.0168	-0.0184	0.0621	-0.0303	0.3758	9.7547	12.0304	27.269
5	5.4104	0.8783	0.3054	4.4725	-0.1704	6.2794	-0.1331	0.4236	0.046	-0.4122	0.1126	-0.3248	-0.0872	-0.0182	0.0205	0.0542	-0.0083	0.0008	0.036	-0.0107	0.0815	-8.5534	-13.4916	18.7741
6	5.808	-0.3759	-2.3967	2.6206	0.5652	4.3474	0.2022	-0.781	0.7775	0.2949	-0.0726	0.549	-0.4914	-0.4108	-0.1296	0.1625	0.0472	0.0091	0.2673	-0.1433	0.4216	-11.0689	-0.2891	36.5504

Refinement TLS group

Selection: ALL

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