PDB-9i3w: Structure of anti-EV71 human monoclonal antibody 16-2-8C Fab

ID or keywords:

Entry

Database: PDB / ID: 9i3w

Title

Structure of anti-EV71 human monoclonal antibody 16-2-8C Fab

Components

heavy chain
light chain

Keywords

ANTIVIRAL PROTEIN / EV71 / antibody / 16-2-8C / Fab

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.14 Å

Authors

Zhou, D. / Ren, J. / Stuart, D.I.

Funding support

United Kingdom, 2items

Citation

Journal: To Be Published
Title: Fine antigenic mapping of human enterovirus 71 from structures of cognate complexes for a panel of 12 patient derived monoclonal antibodies
Authors: Zhou, D. / Ren, J. / Stuart, D.I.

History

Deposition	Jan 24, 2025	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Feb 4, 2026	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9i3w.cif.gz	275.1 KB	Display	PDBx/mmCIF format
PDB format	pdb9i3w.ent.gz	169.1 KB	Display	PDB format
PDBx/mmJSON format	9i3w.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/i3/9i3w ftp://data.pdbj.org/pub/pdb/validation_reports/i3/9i3w	HTTPS FTP

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Related structure data

Related structure data	9i3xC 9i3zC 9i40C 9i41C 9i42C 9i43C 9i45C 9i4bC 9i4cC 9i4dC 9i4eC C: citing same article (ref.)

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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

H: heavy chain

L: light chain

hetero molecules

49.5 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	47.013, 80.394, 57.572
Angle α, β, γ (deg.)	90.000, 93.832, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	heavy chain Mass: 26488.775 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293T / Production host: Homo sapiens (human)
#2: Antibody	light chain Mass: 22676.033 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293T / Production host: Homo sapiens (human)
#3: Chemical	ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER Mass: 209.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₈H₁₉NO₅ / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#4: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₆O₂ / Feature type: SUBJECT OF INVESTIGATION
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 565 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
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: 2.21 Å³/Da / Density % sol: 44.29 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, sitting drop Details: 25% (w/v) PEG 3350, 0.1 M Bis-Tris, pH 6.5, protein concentration: 26.4mg/ml

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9282 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 17, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9282 Å / Relative weight: 1
Reflection	Resolution: 1.14→46.908 Å / Num. obs: 153940 / % possible obs: 99.1 % / Redundancy: 6 % / CC_1/2: 1 / Net I/σ(I): 11.5
Reflection shell	Resolution: 1.14→1.169 Å / Num. unique obs: 7168 / CC_1/2: 0.5

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0419	refinement
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.14→46.908 Å / Cor.coef. F_o:F_c: 0.979 / Cor.coef. F_o:F_c free: 0.973 / SU B: 2.045 / SU ML: 0.038 / Cross valid method: FREE R-VALUE / ESU R: 0.038 / ESU R Free: 0.038
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.1938	7459	4.896 %
R_work	0.1661	144890	-
all	0.168	-	-
obs	-	152349	98.102 %

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: 18.136 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.367 Å²	0 Å²	-0.358 Å²
2-	-	-1.346 Å²	-0 Å²
3-	-	-	1.745 Å²

Refinement step

Cycle: LAST / Resolution: 1.14→46.908 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3352	0	22	565	3939

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.012	3630
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	3314
X-RAY DIFFRACTION	r_angle_refined_deg	1.635	1.794	5027
X-RAY DIFFRACTION	r_angle_other_deg	0.612	1.708	7770
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.935	5	522
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	9.533	5	9
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	10.896	10	563
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	14.323	10	118
X-RAY DIFFRACTION	r_chiral_restr	0.091	0.2	591
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.02	4273
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	767
X-RAY DIFFRACTION	r_nbd_refined	0.216	0.2	453
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.2	0.2	2699
X-RAY DIFFRACTION	r_nbtor_refined	0.162	0.2	1663
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.08	0.2	1688
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.235	0.2	329
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.176	0.2	15
X-RAY DIFFRACTION	r_nbd_other	0.201	0.2	60
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.177	0.2	37
X-RAY DIFFRACTION	r_xyhbond_nbd_other	0.036	0.2	1
X-RAY DIFFRACTION	r_mcbond_it	5.911	1.814	1870
X-RAY DIFFRACTION	r_mcbond_other	5.909	1.814	1870
X-RAY DIFFRACTION	r_mcangle_it	8.534	3.292	2353
X-RAY DIFFRACTION	r_mcangle_other	8.533	3.293	2354
X-RAY DIFFRACTION	r_scbond_it	7.354	2.062	1760
X-RAY DIFFRACTION	r_scbond_other	7.352	2.063	1761
X-RAY DIFFRACTION	r_scangle_it	10.444	3.648	2636
X-RAY DIFFRACTION	r_scangle_other	10.442	3.649	2637
X-RAY DIFFRACTION	r_lrange_it	17.119	24.942	3878
X-RAY DIFFRACTION	r_lrange_other	15.37	21.232	3701
X-RAY DIFFRACTION	r_rigid_bond_restr	3.697	3	6944

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
1.14-1.169	0.388	513	0.388	9821	0.388	11470	0.876	0.863	90.0959	0.383
1.169-1.201	0.388	488	0.362	10133	0.363	11216	0.881	0.9	94.6951	0.352
1.201-1.236	0.364	545	0.338	10080	0.339	10851	0.903	0.913	97.9172	0.326
1.236-1.274	0.337	490	0.314	9823	0.315	10520	0.913	0.931	98.0323	0.295
1.274-1.316	0.315	456	0.289	9560	0.29	10175	0.923	0.945	98.4373	0.265
1.316-1.362	0.273	471	0.248	9307	0.249	9893	0.947	0.958	98.8376	0.22
1.362-1.413	0.23	481	0.213	8957	0.214	9556	0.962	0.97	98.7652	0.185
1.413-1.471	0.228	434	0.194	8702	0.195	9228	0.963	0.975	99.003	0.165
1.471-1.536	0.214	432	0.166	8253	0.169	8765	0.969	0.982	99.0873	0.141
1.536-1.611	0.182	474	0.135	7922	0.138	8443	0.978	0.989	99.4433	0.115
1.611-1.698	0.158	384	0.118	7593	0.12	8021	0.984	0.991	99.4514	0.103
1.698-1.801	0.156	333	0.112	7230	0.114	7601	0.984	0.992	99.5001	0.101
1.801-1.925	0.173	325	0.118	6755	0.12	7111	0.982	0.992	99.5641	0.112
1.925-2.079	0.156	324	0.117	6300	0.118	6643	0.986	0.992	99.714	0.117
2.079-2.277	0.157	334	0.122	5785	0.124	6130	0.984	0.991	99.8206	0.127
2.277-2.545	0.187	272	0.14	5257	0.143	5541	0.979	0.988	99.7834	0.152
2.545-2.937	0.183	271	0.153	4649	0.155	4922	0.98	0.986	99.9594	0.172
2.937-3.594	0.16	211	0.153	3948	0.153	4166	0.985	0.986	99.832	0.18
3.594-5.068	0.164	149	0.146	3066	0.147	3215	0.985	0.988	100	0.185
5.068-46.908	0.182	72	0.181	1749	0.181	1829	0.976	0.98	99.5626	0.228

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