PDB-9i43: Structure of anti-EV71 human monoclonal antibody 16-2-9D Fab

ID or keywords:

Entry

Database: PDB / ID: 9i43

Title

Structure of anti-EV71 human monoclonal antibody 16-2-9D Fab

Components

heavy chain
light chain

Keywords

ANTIVIRAL PROTEIN / EV71 / antibody / 16-2-9D / Fab

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.18 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	9i43.cif.gz	273.7 KB	Display	PDBx/mmCIF format
PDB format	pdb9i43.ent.gz	168.3 KB	Display	PDB format
PDBx/mmJSON format	9i43.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/i4/9i43 ftp://data.pdbj.org/pub/pdb/validation_reports/i4/9i43	HTTPS FTP

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Related structure data

Related structure data	9i3wC 9i3xC 9i3zC 9i40C 9i41C 9i42C 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

49.4 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)	47.743, 80.316, 57.489
Angle α, β, γ (deg.)	90.000, 94.937, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	heavy chain Mass: 26446.584 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: 22678.006 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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₂H₆O₂ / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 606 / 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: 2.24 Å³/Da / Density % sol: 44.98 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, sitting drop / Details: 25% (w/v) PEG 3350, 0.1 M citrate, pH 3.5

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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: Apr 11, 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: 1.18→57.341 Å / Num. obs: 141520 / % possible obs: 100 % / Redundancy: 6.3 % / CC_1/2: 1 / Net I/σ(I): 10.6
Reflection shell	Resolution: 1.18→1.211 Å / Num. unique obs: 7009 / CC_1/2: 0.7

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0419	refinement
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.18→57.341 Å / Cor.coef. F_o:F_c: 0.981 / Cor.coef. F_o:F_c free: 0.975 / SU B: 1.553 / SU ML: 0.03 / Cross valid method: FREE R-VALUE / ESU R: 0.036 / ESU R Free: 0.037
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.1758	7025	4.999 %
R_work	0.1451	133492	-
all	0.147	-	-
obs	-	140517	99.271 %

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: 17.268 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.165 Å²	-0 Å²	0.433 Å²
2-	-	-0.188 Å²	0 Å²
3-	-	-	0.273 Å²

Refinement step

Cycle: LAST / Resolution: 1.18→57.341 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3329	0	20	606	3955

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.012	3579
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	3289
X-RAY DIFFRACTION	r_angle_refined_deg	1.78	1.797	4936
X-RAY DIFFRACTION	r_angle_other_deg	0.663	1.717	7690
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.272	5	501
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	7.686	5	9
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.181	10	557
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	14.883	10	120
X-RAY DIFFRACTION	r_chiral_restr	0.106	0.2	575
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.02	4196
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	756
X-RAY DIFFRACTION	r_nbd_refined	0.222	0.2	445
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.197	0.2	2631
X-RAY DIFFRACTION	r_nbtor_refined	0.163	0.2	1594
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.078	0.2	1685
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.248	0.2	304
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.263	0.2	15
X-RAY DIFFRACTION	r_nbd_other	0.226	0.2	55
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.241	0.2	41
X-RAY DIFFRACTION	r_mcbond_it	5.518	1.685	1840
X-RAY DIFFRACTION	r_mcbond_other	5.513	1.685	1840
X-RAY DIFFRACTION	r_mcangle_it	7.981	3.06	2311
X-RAY DIFFRACTION	r_mcangle_other	7.981	3.062	2312
X-RAY DIFFRACTION	r_scbond_it	7.297	1.946	1739
X-RAY DIFFRACTION	r_scbond_other	7.295	1.947	1740
X-RAY DIFFRACTION	r_scangle_it	10.309	3.433	2596
X-RAY DIFFRACTION	r_scangle_other	10.307	3.434	2597
X-RAY DIFFRACTION	r_lrange_it	18.567	26.074	3770
X-RAY DIFFRACTION	r_lrange_other	18.566	26.073	3770
X-RAY DIFFRACTION	r_rigid_bond_restr	4.137	3	6868

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
1.18-1.211	0.334	551	0.332	9640	0.332	10417	0.915	0.923	97.8305	0.328
1.211-1.244	0.328	502	0.31	9481	0.311	10164	0.917	0.933	98.2192	0.301
1.244-1.28	0.299	486	0.289	9305	0.289	9937	0.938	0.943	98.5307	0.276
1.28-1.319	0.268	492	0.25	8975	0.251	9575	0.953	0.958	98.8721	0.235
1.319-1.362	0.274	448	0.218	8828	0.221	9360	0.949	0.969	99.1026	0.2
1.362-1.41	0.223	443	0.19	8482	0.192	8991	0.967	0.977	99.2659	0.171
1.41-1.463	0.211	430	0.171	8199	0.173	8689	0.97	0.981	99.3095	0.153
1.463-1.523	0.187	408	0.141	7954	0.144	8412	0.978	0.987	99.4056	0.125
1.523-1.591	0.173	388	0.121	7615	0.123	8041	0.982	0.991	99.5274	0.108
1.591-1.668	0.15	359	0.109	7254	0.111	7638	0.986	0.993	99.6727	0.099
1.668-1.758	0.15	356	0.103	6974	0.105	7342	0.986	0.993	99.8366	0.095
1.758-1.865	0.143	324	0.098	6575	0.1	6915	0.988	0.994	99.7686	0.094
1.865-1.994	0.131	347	0.1	6167	0.102	6520	0.989	0.994	99.908	0.098
1.994-2.153	0.148	323	0.111	5720	0.113	6047	0.987	0.993	99.9339	0.112
2.153-2.358	0.145	268	0.115	5304	0.116	5574	0.987	0.992	99.9641	0.119
2.358-2.636	0.167	250	0.13	4791	0.132	5043	0.982	0.99	99.9603	0.138
2.636-3.043	0.17	198	0.138	4289	0.14	4488	0.983	0.988	99.9777	0.151
3.043-3.724	0.168	226	0.144	3568	0.145	3796	0.983	0.988	99.9473	0.164
3.724-5.256	0.148	138	0.128	2801	0.129	2941	0.988	0.991	99.932	0.154
5.256-57.341	0.189	88	0.188	1570	0.188	1659	0.982	0.978	99.9397	0.219

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