PDB-8ef3: Crystal structure of a NHP anti-ZIKV neutralizing antibody rhMZ119-D

ID or keywords:

Entry

Database: PDB / ID: 8ef3

Title

Crystal structure of a NHP anti-ZIKV neutralizing antibody rhMZ119-D

Components

rhMZ119-D antibody heavy chain
rhMZ119-D antibody light chain

Keywords

VIRAL PROTEIN / ZIKV / ZIKV-specific / cross-protomer epitopes

Function / homology

Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta

Function and homology information

Biological species

Macaca mulatta (Rhesus monkey)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.672 Å

Authors

Sankhala, R.S. / Joyce, M.G.

Funding support

United States, 1items

Citation

Journal: Cell Rep / Year: 2023
Title: Zika-specific neutralizing antibodies targeting inter-dimer envelope epitopes.
Authors: Sankhala, R.S. / Dussupt, V. / Donofrio, G. / Gromowski, G.D. / De La Barrera, R.A. / Larocca, R.A. / Mendez-Rivera, L. / Lee, A. / Choe, M. / Zaky, W. / Mantus, G. / Jensen, J.L. / Chen, W. ...

History

Deposition	Sep 7, 2022	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 30, 2023	Provider: repository / Type: Initial release
Revision 1.1	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	8ef3.cif.gz	351.2 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	8ef3_validation.pdf.gz	446 KB	Display	wwPDB validaton report
Full document	8ef3_full_validation.pdf.gz	452.1 KB	Display
Data in XML	8ef3_validation.xml.gz	41.5 KB	Display
Data in CIF	8ef3_validation.cif.gz	63.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ef/8ef3 ftp://data.pdbj.org/pub/pdb/validation_reports/ef/8ef3	HTTPS FTP

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Related structure data

Related structure data	8ee5C 8ee8C 8eedC 8eeeC 8eezC 8ef0C 8ef1C 8ef2C 5qf1S 5tz2S S: Starting model for refinement 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

A: rhMZ119-D antibody heavy chain

B: rhMZ119-D antibody light chain

C: rhMZ119-D antibody heavy chain

D: rhMZ119-D antibody light chain

92.2 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: rhMZ119-D antibody heavy chain

B: rhMZ119-D antibody light chain

defined by author&software
Evidence: native gel electrophoresis, reduced and native SDS PAGE
46.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: rhMZ119-D antibody heavy chain

D: rhMZ119-D antibody light chain

defined by author&software
46.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	70.243, 71.015, 103.741
Angle α, β, γ (deg.)	90.000, 102.380, 90.000
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	chain A
2	1	chain C
1	2	(chain B and (resid 1 through 52 or resid 54 through 211))
2	2	(chain D and (resid 1 through 52 or resid 54 through 211))

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	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	GLU	GLU	GLU	GLU	chain A	A	A	1 - 218	1 - 218
2	1	1	GLU	GLU	GLU	GLU	chain C	C	C	1 - 218	1 - 218
1	1	2	SER	SER	LYS	LYS	(chain B and (resid 1 through 52 or resid 54 through 211))	B	B	1 - 52	1 - 52
1	2	2	PRO	PRO	ALA	ALA	(chain B and (resid 1 through 52 or resid 54 through 211))	B	B	54 - 211	54 - 211
2	1	2	SER	SER	LYS	LYS	(chain D and (resid 1 through 52 or resid 54 through 211))	D	D	1 - 52	1 - 52
2	2	2	PRO	PRO	ALA	ALA	(chain D and (resid 1 through 52 or resid 54 through 211))	D	D	54 - 211	54 - 211

NCS ensembles :

ID
1
2

#1: Antibody	rhMZ119-D antibody heavy chain Mass: 23538.344 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Production host: Homo sapiens (human)
#2: Antibody	rhMZ119-D antibody light chain Mass: 22573.865 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Production host: Homo sapiens (human)
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1012 / 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: 2.74 Å³/Da / Density % sol: 55.12 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 18% PEG 8K, 0.2M CaAc hydrate, 0.1M Na Cacodylate (pH6.5)

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97 Å
Detector	Type: ADSC QUANTUM 210 / Detector: CCD / Date: Aug 16, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97 Å / Relative weight: 1
Reflection	Resolution: 1.67→50 Å / Num. obs: 114507 / % possible obs: 99.3 % / Redundancy: 3.7 % / CC_1/2: 0.85 / R_sym value: 0.062 / Net I/σ(I): 21.2
Reflection shell	Resolution: 1.67→1.73 Å / Num. unique obs: 11124 / CC_1/2: 0.35 / R_sym value: 1.118

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Processing

Software

Name	Version	Classification
PHENIX	1.11.1_2575	refinement
PDB_EXTRACT	3.27	data extraction
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5TZ2, 5QF1

5tz2

5qf1

Resolution: 1.672→34.305 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.99 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1981	1999	1.89 %
R_work	0.1819	104011	-
obs	0.1822	106010	91.94 %

Solvent computation

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

Displacement parameters

B_iso max: 91.01 Å² / B_iso mean: 22.9508 Å² / B_iso min: 5.06 Å²

Refinement step

Cycle: final / Resolution: 1.672→34.305 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6362	0	0	1012	7374
B_iso mean	-	-	-	35.94	-
Num. residues	-	-	-	-	852

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	6540
X-RAY DIFFRACTION	f_angle_d	0.734	8926
X-RAY DIFFRACTION	f_chiral_restr	0.05	1008
X-RAY DIFFRACTION	f_plane_restr	0.005	1134
X-RAY DIFFRACTION	f_dihedral_angle_d	11.4	3914

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Rms	Type
1	1	A	1933	X-RAY DIFFRACTION	5.354	TORSIONAL
1	2	C	1933	X-RAY DIFFRACTION	5.354	TORSIONAL
2	1	B	1900	X-RAY DIFFRACTION	5.354	TORSIONAL
2	2	D	1900	X-RAY DIFFRACTION	5.354	TORSIONAL

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	% reflection obs (%)
1.672-1.7134	0.2965	45	0.2874	2364	29
1.7134-1.7597	0.2763	103	0.259	5349	67
1.7597-1.8115	0.2825	149	0.2505	7712	96
1.8115-1.8699	0.2592	151	0.2275	7898	99
1.8699-1.9368	0.237	153	0.1945	7972	99
1.9368-2.0143	0.2087	155	0.1798	8011	99
2.0143-2.106	0.206	154	0.1742	8015	100
2.106-2.217	0.1903	154	0.1689	8059	100
2.217-2.3558	0.1849	155	0.1731	8020	100
2.3558-2.5377	0.2187	156	0.1849	8072	100
2.5377-2.793	0.2021	155	0.185	8079	100
2.793-3.1968	0.174	156	0.174	8106	100
3.1968-4.0267	0.1763	156	0.1636	8136	100
4.0267-34.305	0.1752	157	0.1734	8218	99

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	0.8656	0.0407	0.1199	1.4374	0.03	1.2391	-0.0371	-0.0555	0.0513	0.0037	0.0349	0.1171	0.0373	-0.2705	0.0078	0.108	-0.0043	0.001	0.1547	-0.0132	0.0666	39.8395	28.4525	-13.3672
2	1.1176	-0.1626	-0.3939	1.4122	-0.1658	1.3404	0.0051	0.0934	-0.2038	-0.048	0.0202	0.1394	0.0494	0.0166	-0.0177	0.0746	0.025	0.0027	0.0491	-0.0031	0.1071	43.4582	20.3344	-48.8347
3	1.2907	0.1016	-0.2829	2.535	0.4316	1.5065	-0.0108	0.195	-0.2004	-0.2028	-0.029	0.1706	0.0392	-0.204	0.1096	0.1389	0.039	-0.0181	0.089	-0.0312	0.1335	39.1406	24.842	-56.3686
4	0.7712	-0.8549	-0.388	1.1281	-0.0909	1.7001	-0.1894	0.131	-0.1442	-0.1883	0.1589	-0.2376	0.398	-0.0632	0.0369	0.2392	-0.0758	0.0854	0.1639	-0.004	0.1457	41.3094	1.3833	-16.8012
5	1.7026	0.0299	0.5644	1.3663	-0.1427	1.4875	-0.2847	-0.0299	-0.087	-0.0415	0.1495	0.1943	0.0643	-0.3281	-0.0665	0.1518	-0.0593	0.0406	0.201	0.0159	0.1181	34.5395	7.3851	-11.6682
6	0.1417	0.0527	0.1526	0.0231	0.0427	0.2154	-0.0501	-0.0295	-0.0831	0.0575	-0.1518	0.0834	0.2501	-0.311	-0.2316	0.1742	-0.0986	0.0474	0.1663	-0.0306	0.1307	39.0933	3.4752	-27.2873
7	0.5825	0.1192	0.0686	0.8112	0.1893	0.8676	0.061	0.0364	0.217	-0.0368	-0.0387	-0.0156	-0.0643	0.0357	-0.0026	0.0472	-0.0039	0.0167	0.0568	0.0343	0.1211	52.9823	11.2096	-46.9693
8	0.4081	-0.1461	0.327	0.8064	0.3003	0.514	0.0451	0.054	0.0859	-0.0127	-0.0136	-0.0044	0.0233	-0.0881	0.068	0.0307	-0.0016	0.0255	0.066	0.0378	0.1102	51.7652	8.2322	-46.2264
9	0.8781	-0.0445	-0.1088	1.3049	0.0183	1.0684	-0.0519	-0.0143	-0.1189	0.1912	0.0637	0.017	0.0133	0.1098	-0.0128	0.093	0.0449	-0.0052	0.1371	-0.0004	0.1239	9.5564	-5.7535	-37.1166
10	1.9221	0.2064	0.2753	1.6878	-0.4759	1.5958	-0.0165	-0.0515	0.2499	0.0256	0.023	0.2243	0.0976	-0.0499	-0.0282	0.1925	0.005	-0.0423	0.0895	-0	0.1831	-3.8659	-1.0905	-1.7228
11	0.7647	-0.309	0.086	1.5253	0.0314	1.4613	-0.1833	-0.063	0.138	0.2085	0.0535	-0.0998	-0.1469	0.0675	-0.0312	0.0814	-0.0336	-0.0483	0.1376	0.0018	0.1482	7.8809	17.7868	-38.368
12	0.3312	0.1211	-0.069	0.1604	-0.4553	1.5714	-0.0531	0.0497	-0.0741	0.0888	-0.0365	-0.0278	-0.2374	-0.1094	0.0471	0.1308	0.0197	-0.0248	0.1223	-0.0049	0.1229	5.9839	11.97	-20.9349
13	0.9368	-0.5682	0.0107	1.3538	-0.4567	1.1813	0.0348	0.037	0.1594	-0.1891	-0.0908	-0.1097	-0.1597	-0.0066	0.0702	0.1758	0.0039	-0.043	0.0735	0.027	0.123	8.0775	11.7754	-2.2671

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 118 )	A	1 - 118
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 119 through 191 )	A	119 - 191
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 192 through 218 )	A	192 - 218
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 1 through 23 )	B	1 - 23
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 24 through 96 )	B	24 - 96
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 97 through 115 )	B	97 - 115
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 116 through 163 )	B	116 - 163
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 164 through 211 )	B	164 - 211
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 1 through 118 )	C	1 - 118
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 119 through 218 )	C	119 - 218
11	X-RAY DIFFRACTION	11	chain 'D' and (resid 1 through 74 )	D	1 - 74
12	X-RAY DIFFRACTION	12	chain 'D' and (resid 75 through 130 )	D	75 - 130
13	X-RAY DIFFRACTION	13	chain 'D' and (resid 131 through 211 )	D	131 - 211

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