PDB-6a3w: Complex structure of 4-1BB and utomilumab

ID or keywords:

Entry

Database: PDB / ID: 6a3w

Title

Complex structure of 4-1BB and utomilumab

Components

Tumor necrosis factor receptor superfamily member 9
utomilumab VH
utomilumab VL

Keywords

IMMUNE SYSTEM / complex structure / 4-1BB / angonist monoclonal antibody

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: 2 Å

Authors

Li, Y. / Tan, S. / Zhang, C. / Chai, Y. / Qi, J. / Tien, P. / Gao, S. / Gao, G.F.

Citation

Journal: Cell Rep / Year: 2018
Title: Limited Cross-Linking of 4-1BB by 4-1BB Ligand and the Agonist Monoclonal Antibody Utomilumab.
Authors: Li, Y. / Tan, S. / Zhang, C. / Chai, Y. / He, M. / Zhang, C.W. / Wang, Q. / Tong, Z. / Liu, K. / Lei, Y. / Liu, W.J. / Liu, Y. / Tian, Z. / Cao, X. / Yan, J. / Qi, J. / Tien, P. / Gao, S. / Gao, G.F.

History

Deposition	Jun 17, 2018	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Oct 10, 2018	Provider: repository / Type: Initial release
Revision 1.1	Apr 24, 2019	Group: Data collection / Database references / Structure summary Category: citation / citation_author / entity Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _entity.formula_weight
Revision 1.2	Jul 29, 2020	Group: Data collection / Derived calculations / Structure summary Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3	Nov 22, 2023	Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4	Oct 23, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6a3w.cif.gz	544.4 KB	Display	PDBx/mmCIF format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/a3/6a3w ftp://data.pdbj.org/pub/pdb/validation_reports/a3/6a3w	HTTPS FTP

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Related structure data

Related structure data	6a3vC 5grjS 5l36S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6w1h-d 3vh3-d 2z0y-d 6tn3-1 5obl-2 4i7l-d 2yqj-1 5ma9-4 5nuh-d 4i7n-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

6a3vC

5grjS

5l36S

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

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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: utomilumab VH

B: utomilumab VL

C: Tumor necrosis factor receptor superfamily member 9

D: utomilumab VH

E: utomilumab VL

F: Tumor necrosis factor receptor superfamily member 9

G: utomilumab VH

H: utomilumab VL

I: Tumor necrosis factor receptor superfamily member 9

J: utomilumab VH

K: utomilumab VL

L: Tumor necrosis factor receptor superfamily member 9

hetero molecules

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

1

A: utomilumab VH

B: utomilumab VL

C: Tumor necrosis factor receptor superfamily member 9

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

2

D: utomilumab VH

E: utomilumab VL

F: Tumor necrosis factor receptor superfamily member 9

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

3

G: utomilumab VH

H: utomilumab VL

I: Tumor necrosis factor receptor superfamily member 9

hetero molecules

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

4

J: utomilumab VH

K: utomilumab VL

L: Tumor necrosis factor receptor superfamily member 9

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

Unit cell

Length a, b, c (Å)	50.727, 184.604, 90.205
Angle α, β, γ (deg.)	90.00, 104.04, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Antibody

utomilumab VH

Mass: 12869.381 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Homo sapiens (human) / Production host:

Escherichia coli BL21(DE3) (bacteria)

#2: Antibody

utomilumab VL

Mass: 11543.633 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Homo sapiens (human) / Production host:

Escherichia coli BL21(DE3) (bacteria)

#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: 17523.689 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Homo sapiens (human) / Gene: TNFRSF9, CD137, ILA / Production host:

Baculovirus transfer vector pFASTBAC1 / References: UniProt: Q07011

#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: isolated from a genetically manipulated source
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.: 1196 / 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: 2.44 Å³/Da / Density % sol: 49.64 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 0.2M lithium chloride, 0.1M Tris, pH 8.0, 20% w/v PEG 8000

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9792 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 2, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9792 Å / Relative weight: 1
Reflection	Resolution: 2→39.537 Å / Num. obs: 102833 / % possible obs: 95.02 % / Redundancy: 6.3 % / R_pim(I) all: 0.066 / Net I/σ(I): 12.3
Reflection shell	Resolution: 2→2.07 Å

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Processing

Software

Name	Version	Classification
PHENIX	(1.12_2829: ???)	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5L36 and 5GRJ

5l36

5grj

Resolution: 2→39.537 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.15 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2149	5047	4.91 %
R_work	0.1845	-	-
obs	0.186	102833	95.02 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2→39.537 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10320	0	14	1196	11530

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	10617
X-RAY DIFFRACTION	f_angle_d	0.596	14392
X-RAY DIFFRACTION	f_dihedral_angle_d	24.723	3950
X-RAY DIFFRACTION	f_chiral_restr	0.044	1515
X-RAY DIFFRACTION	f_plane_restr	0.004	1861

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 (%)
1.9996-2.0223	0.3079	103	0.2487	1804	X-RAY DIFFRACTION	52
2.0223-2.0461	0.2859	147	0.2327	2626	X-RAY DIFFRACTION	77
2.0461-2.071	0.2521	150	0.2375	3095	X-RAY DIFFRACTION	91
2.071-2.0973	0.2941	180	0.2306	3254	X-RAY DIFFRACTION	94
2.0973-2.1249	0.2581	186	0.2209	3215	X-RAY DIFFRACTION	95
2.1249-2.154	0.2549	177	0.2146	3266	X-RAY DIFFRACTION	97
2.154-2.1847	0.2413	170	0.2055	3315	X-RAY DIFFRACTION	96
2.1847-2.2173	0.2616	156	0.2132	3255	X-RAY DIFFRACTION	95
2.2173-2.252	0.2497	178	0.2062	3304	X-RAY DIFFRACTION	97
2.252-2.2889	0.2362	181	0.2117	3296	X-RAY DIFFRACTION	96
2.2889-2.3284	0.2533	161	0.2158	3273	X-RAY DIFFRACTION	96
2.3284-2.3707	0.2673	188	0.2142	3324	X-RAY DIFFRACTION	97
2.3707-2.4163	0.2554	162	0.2104	3274	X-RAY DIFFRACTION	95
2.4163-2.4656	0.2898	189	0.2089	3284	X-RAY DIFFRACTION	98
2.4656-2.5192	0.2223	163	0.2115	3334	X-RAY DIFFRACTION	96
2.5192-2.5778	0.2571	171	0.1979	3301	X-RAY DIFFRACTION	96
2.5778-2.6423	0.242	196	0.1988	3290	X-RAY DIFFRACTION	97
2.6423-2.7137	0.2373	180	0.1995	3319	X-RAY DIFFRACTION	97
2.7137-2.7935	0.2327	193	0.1903	3318	X-RAY DIFFRACTION	98
2.7935-2.8836	0.2438	179	0.2023	3340	X-RAY DIFFRACTION	98
2.8836-2.9867	0.2254	180	0.1939	3407	X-RAY DIFFRACTION	98
2.9867-3.1062	0.2358	173	0.1836	3362	X-RAY DIFFRACTION	99
3.1062-3.2475	0.2232	170	0.187	3392	X-RAY DIFFRACTION	99
3.2475-3.4186	0.1826	159	0.1749	3421	X-RAY DIFFRACTION	99
3.4186-3.6327	0.1913	148	0.1663	3446	X-RAY DIFFRACTION	99
3.6327-3.913	0.1721	176	0.1607	3446	X-RAY DIFFRACTION	99
3.913-4.3063	0.1812	178	0.1477	3380	X-RAY DIFFRACTION	100
4.3063-4.9284	0.1431	127	0.1358	3483	X-RAY DIFFRACTION	100
4.9284-6.2054	0.1746	168	0.1644	3472	X-RAY DIFFRACTION	100
6.2054-39.5448	0.1882	158	0.1974	3490	X-RAY DIFFRACTION	100

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	0.557	0.161	-0.2007	0.6152	-0.1174	0.2201	0.0367	-0.0493	0.0304	0.0322	-0.0238	-0.0505	0.0019	0.077	-0	0.1078	-0.004	-0.005	0.1445	0.0103	0.1126	6.3762	102.3606	-56.6761
2	0.749	-0.0407	-0.0101	0.4934	-0.3207	0.6774	0.0359	0.0609	-0.0427	-0.0582	0.0019	0.0504	0.0539	-0.0715	-0	0.1381	0.0003	-0.0116	0.1384	0.0012	0.1449	-13.5116	97.6759	-66.4587
3	0.8913	-0.0772	0.2714	0.0618	0.0743	0.2665	0.0113	-0.1191	0.0086	0.0055	-0.0264	0.0421	-0.0631	0.0575	-0.001	0.2348	-0.015	0.0048	0.1846	0.03	0.164	-13.6671	98.0903	-46.4124
4	0.7703	-0.2257	-0.053	0.6337	0.108	0.3284	0.0724	0.0214	-0.0528	-0.1025	-0.0392	-0.1102	-0.0075	0.0697	-0	0.229	0.0078	0.0044	0.2531	-0.0038	0.249	7.0202	49.7552	-49.2263
5	0.7095	0.0014	0.0186	0.5781	-0.2187	0.636	0.0336	-0.1712	-0.009	0.0378	-0.0658	0.0461	-0.0559	0.0351	-0	0.2382	-0.0058	0.0008	0.2355	-0.011	0.2747	-12.6651	54.4087	-39.3555
6	0.1893	-0.1188	-0.0949	0.4487	-0.1535	0.8076	0.0288	0.2903	0.028	-0.2654	0.0622	0.1212	0.0511	-0.0424	0	0.3372	-0.0076	-0.0229	0.3164	0.0195	0.268	-6.8063	62.5226	-62.0837
7	0.6234	-0.2232	-0.0208	0.789	0.0453	0.2272	-0.02	0.0228	0.0386	-0.0322	-0.0037	0.105	0.0008	-0.0651	-0	0.1025	-0.0047	-0.0073	0.1463	-0.0166	0.1114	-9.7115	92.414	-15.4197
8	0.6855	0.2505	0.1345	0.6644	0.4223	0.5525	0.0267	-0.0787	-0.0102	0.0429	-0.0312	0.0097	0.0739	-0.0119	0	0.1551	-0.0072	-0.0079	0.1637	0.0084	0.1381	9.9032	90.9172	-4.5083
9	0.7143	0.0572	-0.454	0.089	-0.1942	0.5762	0.0853	0.111	0.0418	0.0405	-0.0468	-0.0162	-0.0588	-0.0069	0.0003	0.2509	-0.0156	0.0127	0.2198	-0.0074	0.208	8.7127	82.7491	-24.2063
10	0.7015	0.1272	-0.2525	0.799	-0.0848	0.382	0.0389	0.0339	-0.1079	0.0666	-0.0199	0.0375	0.0082	-0.0513	-0	0.1404	-0.0001	-0.005	0.144	-0.0175	0.163	-9.106	40.2966	-0.8675
11	0.763	-0.4558	-0.2571	0.731	0.519	0.8903	0.057	0.1088	-0.0239	-0.0595	-0.0132	0.0036	-0.0732	-0.0118	-0	0.1586	0.0036	0.0072	0.1599	-0.0098	0.1985	10.5244	39.5079	-11.8662
12	0.5895	-0.3417	-0.0514	0.2559	-0.1662	0.3019	-0.0173	-0.0634	0.0308	0.0966	-0.0092	-0.0069	-0.0522	0.0093	-0	0.2521	-0.0136	0.0074	0.1836	-0.0197	0.2325	10.2747	51.7456	6.2596

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain A
2	X-RAY DIFFRACTION	2	chain B
3	X-RAY DIFFRACTION	3	chain C
4	X-RAY DIFFRACTION	4	chain D
5	X-RAY DIFFRACTION	5	chain E
6	X-RAY DIFFRACTION	6	chain F
7	X-RAY DIFFRACTION	7	chain G
8	X-RAY DIFFRACTION	8	chain H
9	X-RAY DIFFRACTION	9	chain I
10	X-RAY DIFFRACTION	10	chain J
11	X-RAY DIFFRACTION	11	chain K
12	X-RAY DIFFRACTION	12	chain L

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