PDB-9gwz: Crystal structure of 23ME-00610 Fab

ID or keywords:

Entry

Database: PDB / ID: 9gwz

Title

Crystal structure of 23ME-00610 Fab

Components

(23ME-00610 Fab ...) x 2

Keywords

ANTITUMOR PROTEIN / 23ME-00610 / human CD200R1 / immune checkpoint inhibitor / immuno-oncology

Function / homology

PHOSPHATE ION

Function and homology information

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.12 Å

Authors

Huang, Y.M. / Ganichkin, O.M.

Funding support

1items

Citation

Journal: Mabs / Year: 2024
Title: CD200R1 immune checkpoint blockade by the first-in-human anti-CD200R1 antibody 23ME-00610: molecular mechanism and engineering of a surrogate antibody.
Authors: Melero, C. / Budiardjo, S.J. / Daruwalla, A. / Larrabee, L. / Ganichkin, O. / Heiler, A.J. / Fenaux, J. / Chung, B. / Fuh, G. / Huang, Y.M.

History

Deposition	Sep 27, 2024	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Oct 23, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9gwz.cif.gz	370 KB	Display	PDBx/mmCIF format
PDB format	pdb9gwz.ent.gz		Display	PDB format
PDBx/mmJSON format	9gwz.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9gwz_validation.pdf.gz	511.7 KB	Display	wwPDB validaton report
Full document	9gwz_full_validation.pdf.gz	520.2 KB	Display
Data in XML	9gwz_validation.xml.gz	76.6 KB	Display
Data in CIF	9gwz_validation.cif.gz	100.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/gw/9gwz ftp://data.pdbj.org/pub/pdb/validation_reports/gw/9gwz	HTTPS FTP

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Related structure data

Related structure data	9gwtC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&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)

Deposited unit

HHH: 23ME-00610 Fab (heavy)

LLL: 23ME-00610 Fab (light)

AAA: 23ME-00610 Fab (heavy)

BBB: 23ME-00610 Fab (light)

CCC: 23ME-00610 Fab (heavy)

DDD: 23ME-00610 Fab (light)

EEE: 23ME-00610 Fab (heavy)

FFF: 23ME-00610 Fab (light)

hetero molecules

197 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

HHH: 23ME-00610 Fab (heavy)

LLL: 23ME-00610 Fab (light)

hetero molecules

defined by author&software
Evidence: gel filtration
49.2 kDa, 2 polymers

2

AAA: 23ME-00610 Fab (heavy)

BBB: 23ME-00610 Fab (light)

hetero molecules

defined by author&software
49.2 kDa, 2 polymers

3

CCC: 23ME-00610 Fab (heavy)

DDD: 23ME-00610 Fab (light)

hetero molecules

defined by author&software
49.2 kDa, 2 polymers

4

EEE: 23ME-00610 Fab (heavy)

FFF: 23ME-00610 Fab (light)

hetero molecules

defined by author&software
49.1 kDa, 2 polymers

Unit cell

Length a, b, c (Å)	225.274, 67.447, 136.880
Angle α, β, γ (deg.)	90.000, 101.710, 90.000
Int Tables number	5
Space group name H-M	C121

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Dom-ID	Component-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	1	GLU	GLU	LYS	LYS	HHH	A	1 - 219	1 - 219
2	2	1	GLU	GLU	LYS	LYS	AAA	C	1 - 219	1 - 219
3	3	2	GLU	GLU	LYS	LYS	HHH	A	1 - 219	1 - 219
4	4	2	GLU	GLU	LYS	LYS	CCC	E	1 - 219	1 - 219
5	5	3	GLU	GLU	PRO	PRO	HHH	A	1 - 218	1 - 218
6	6	3	GLU	GLU	PRO	PRO	EEE	G	1 - 218	1 - 218
7	7	4	ASP	ASP	GLY	GLY	LLL	B	1 - 216	1 - 216
8	8	4	ASP	ASP	GLY	GLY	BBB	D	1 - 216	1 - 216
9	9	5	ASP	ASP	GLY	GLY	LLL	B	1 - 216	1 - 216
10	10	5	ASP	ASP	GLY	GLY	DDD	F	1 - 216	1 - 216
11	11	6	ASP	ASP	GLY	GLY	LLL	B	1 - 216	1 - 216
12	12	6	ASP	ASP	GLY	GLY	FFF	H	1 - 216	1 - 216
13	13	7	GLU	GLU	LYS	LYS	AAA	C	1 - 219	1 - 219
14	14	7	GLU	GLU	LYS	LYS	CCC	E	1 - 219	1 - 219
15	15	8	GLU	GLU	PRO	PRO	AAA	C	1 - 218	1 - 218
16	16	8	GLU	GLU	PRO	PRO	EEE	G	1 - 218	1 - 218
17	17	9	ASP	ASP	GLU	GLU	BBB	D	1 - 217	1 - 217
18	18	9	ASP	ASP	GLU	GLU	DDD	F	1 - 217	1 - 217
19	19	10	ASP	ASP	GLU	GLU	BBB	D	1 - 217	1 - 217
20	20	10	ASP	ASP	GLU	GLU	FFF	H	1 - 217	1 - 217
21	21	11	GLU	GLU	PRO	PRO	CCC	E	1 - 218	1 - 218
22	22	11	GLU	GLU	PRO	PRO	EEE	G	1 - 218	1 - 218
23	23	12	ASP	ASP	GLU	GLU	DDD	F	1 - 217	1 - 217
24	24	12	ASP	ASP	GLU	GLU	FFF	H	1 - 217	1 - 217

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
4	Local NCS retraints between domains: 7 8
5	Local NCS retraints between domains: 9 10
6	Local NCS retraints between domains: 11 12
7	Local NCS retraints between domains: 13 14
8	Local NCS retraints between domains: 15 16
9	Local NCS retraints between domains: 17 18
10	Local NCS retraints between domains: 19 20
11	Local NCS retraints between domains: 21 22
12	Local NCS retraints between domains: 23 24

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Antibody , 2 types, 8 molecules HHHAAACCCEEELLLBBBDDDFFF

#1: Antibody	23ME-00610 Fab (heavy) / 23ME-00610 Fab Mass: 24980.053 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: Heavy chain / Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): Expi293 / Production host: Homo sapiens (human)
#2: Antibody	23ME-00610 Fab (light) / 23ME-00610 Fab Mass: 23887.381 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: Light chain / Source: (gene. exp.) Homo sapiens (human) / Cell (production host): Expi293 / Production host: Homo sapiens (human)

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Non-polymers , 4 types, 765 molecules

#3: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#4: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO₄
#5: Chemical	ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₆H₁₄O₂ / Comment: precipitant*YM
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 749 / Source method: isolated from a natural source / Formula: H₂O

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Details

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: 2.6 Å³/Da / Density % sol: 52.78 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: MPD 50.0% v/v; NH4H2PO4 0.20M; Tris-HCL 0.10M pH 8.50

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99 Å
Detector	Type: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: May 19, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.99 Å / Relative weight: 1
Reflection	Resolution: 2.12→95.167 Å / Num. obs: 112044 / % possible obs: 97.8 % / Redundancy: 7.4 % / CC_1/2: 0.989 / R_merge(I) obs: 0.159 / Net I/σ(I): 7.8
Reflection shell	Resolution: 2.12→2.157 Å / R_merge(I) obs: 1.178 / Num. unique obs: 5684 / CC_1/2: 0.46

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
autoPROC		data reduction
autoPROC		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.12→67.106 Å / Cor.coef. F_o:F_c: 0.951 / Cor.coef. F_o:F_c free: 0.918 / SU B: 8.337 / SU ML: 0.198 / Cross valid method: FREE R-VALUE / ESU R: 0.252 / ESU R Free: 0.203
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2562	5592	5.004 %
R_work	0.2182	106164	-
all	0.22	-	-
obs	-	111756	97.543 %

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: 43.299 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	3.704 Å²	-0 Å²	-2.166 Å²
2-	-	-1.222 Å²	-0 Å²
3-	-	-	-1.459 Å²

Refinement step

Cycle: LAST / Resolution: 2.12→67.106 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13091	0	61	749	13901

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.004	0.013	13653
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.017	12496
X-RAY DIFFRACTION	r_ext_dist_refined_d	0.599	0.05	7
X-RAY DIFFRACTION	r_angle_refined_deg	1.391	1.642	18666
X-RAY DIFFRACTION	r_angle_other_deg	1.105	1.571	28955
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.572	5	1777
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.298	23.596	570
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.995	15	2154
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.149	15	48
X-RAY DIFFRACTION	r_chiral_restr	0.048	0.2	1813
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	15631
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	2973
X-RAY DIFFRACTION	r_nbd_refined	0.147	0.2	1784
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.151	0.2	10818
X-RAY DIFFRACTION	r_nbtor_refined	0.141	0.2	6164
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.067	0.2	6089
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.135	0.2	732
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.075	0.2	15
X-RAY DIFFRACTION	r_nbd_other	0.151	0.2	108
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.13	0.2	23
X-RAY DIFFRACTION	r_mcbond_it	1.967	4.588	7057
X-RAY DIFFRACTION	r_mcbond_other	1.967	4.588	7056
X-RAY DIFFRACTION	r_mcangle_it	3.174	6.863	8851
X-RAY DIFFRACTION	r_mcangle_other	3.174	6.864	8852
X-RAY DIFFRACTION	r_scbond_it	2.022	4.746	6596
X-RAY DIFFRACTION	r_scbond_other	2.022	4.746	6597
X-RAY DIFFRACTION	r_scangle_it	3.26	7.031	9815
X-RAY DIFFRACTION	r_scangle_other	3.26	7.031	9816
X-RAY DIFFRACTION	r_lrange_it	5.634	52.104	13841
X-RAY DIFFRACTION	r_lrange_other	5.598	51.995	13723
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.027	0.05	2224
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.03	0.05	2199
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.023	0.05	2182
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.019	0.05	2413
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.015	0.05	2394
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.019	0.05	2392
X-RAY DIFFRACTION	r_ncsr_local_group_7	0.025	0.05	2177
X-RAY DIFFRACTION	r_ncsr_local_group_8	0.031	0.05	2188
X-RAY DIFFRACTION	r_ncsr_local_group_9	0.017	0.05	2395
X-RAY DIFFRACTION	r_ncsr_local_group_10	0.015	0.05	2409
X-RAY DIFFRACTION	r_ncsr_local_group_11	0.03	0.05	2185
X-RAY DIFFRACTION	r_ncsr_local_group_12	0.015	0.05	2431

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	HHH	X-RAY DIFFRACTION	Local ncs	0.02703	0.05
1	2	AAA	X-RAY DIFFRACTION	Local ncs	0.02703	0.05
2	3	HHH	X-RAY DIFFRACTION	Local ncs	0.0299	0.05
2	4	CCC	X-RAY DIFFRACTION	Local ncs	0.0299	0.05
3	5	HHH	X-RAY DIFFRACTION	Local ncs	0.02252	0.05
3	6	EEE	X-RAY DIFFRACTION	Local ncs	0.02252	0.05
4	7	LLL	X-RAY DIFFRACTION	Local ncs	0.01922	0.05
4	8	BBB	X-RAY DIFFRACTION	Local ncs	0.01922	0.05
5	9	LLL	X-RAY DIFFRACTION	Local ncs	0.0153	0.05
5	10	DDD	X-RAY DIFFRACTION	Local ncs	0.0153	0.05
6	11	LLL	X-RAY DIFFRACTION	Local ncs	0.01928	0.05
6	12	FFF	X-RAY DIFFRACTION	Local ncs	0.01928	0.05
7	13	AAA	X-RAY DIFFRACTION	Local ncs	0.02466	0.05
7	14	CCC	X-RAY DIFFRACTION	Local ncs	0.02466	0.05
8	15	AAA	X-RAY DIFFRACTION	Local ncs	0.03096	0.05
8	16	EEE	X-RAY DIFFRACTION	Local ncs	0.03096	0.05
9	17	BBB	X-RAY DIFFRACTION	Local ncs	0.01694	0.05
9	18	DDD	X-RAY DIFFRACTION	Local ncs	0.01694	0.05
10	19	BBB	X-RAY DIFFRACTION	Local ncs	0.01451	0.05
10	20	FFF	X-RAY DIFFRACTION	Local ncs	0.01451	0.05
11	21	CCC	X-RAY DIFFRACTION	Local ncs	0.03029	0.05
11	22	EEE	X-RAY DIFFRACTION	Local ncs	0.03029	0.05
12	23	DDD	X-RAY DIFFRACTION	Local ncs	0.01478	0.05
12	24	FFF	X-RAY DIFFRACTION	Local ncs	0.01478	0.05

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 (%)
2.12-2.175	0.384	439	0.392	7813	X-RAY DIFFRACTION	97.5875
2.175-2.235	0.385	405	0.366	7699	X-RAY DIFFRACTION	98.8654
2.235-2.299	0.379	268	0.349	5286	X-RAY DIFFRACTION	69.6863
2.299-2.37	0.312	431	0.295	7303	X-RAY DIFFRACTION	99.9871
2.37-2.448	0.292	363	0.27	7167	X-RAY DIFFRACTION	100
2.448-2.534	0.304	386	0.26	6897	X-RAY DIFFRACTION	99.9863
2.534-2.629	0.28	343	0.241	6680	X-RAY DIFFRACTION	100
2.629-2.737	0.281	310	0.242	6463	X-RAY DIFFRACTION	99.9262
2.737-2.858	0.246	330	0.212	6156	X-RAY DIFFRACTION	100
2.858-2.998	0.265	311	0.213	5889	X-RAY DIFFRACTION	100
2.998-3.16	0.254	294	0.217	5602	X-RAY DIFFRACTION	99.983
3.16-3.351	0.267	287	0.215	5342	X-RAY DIFFRACTION	99.9645
3.351-3.583	0.254	269	0.215	4960	X-RAY DIFFRACTION	99.4296
3.583-3.869	0.214	229	0.198	4667	X-RAY DIFFRACTION	99.4112
3.869-4.238	0.209	226	0.184	4292	X-RAY DIFFRACTION	99.6471
4.238-4.738	0.191	197	0.157	3910	X-RAY DIFFRACTION	99.9757
4.738-5.47	0.234	186	0.181	3456	X-RAY DIFFRACTION	99.9177
5.47-6.697	0.226	148	0.216	2941	X-RAY DIFFRACTION	99.9353
6.697-9.459	0.22	107	0.174	2326	X-RAY DIFFRACTION	99.9179
9.459-67.106	0.327	63	0.217	1315	X-RAY DIFFRACTION	99.3511

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