PDB-9i41: Structure of anti-EV71 human monoclonal antibody 16-3-3C Fab

ID or keywords:

Entry

Database: PDB / ID: 9i41

Title

Structure of anti-EV71 human monoclonal antibody 16-3-3C Fab

Components

heavy chain
light chain

Keywords

ANTIVIRAL PROTEIN / EV71 / antibody / 16-3-3C / Fab

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.32 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

-
Download

PDBx/mmCIF format	9i41.cif.gz	269.6 KB	Display	PDBx/mmCIF format
PDB format	pdb9i41.ent.gz	166.3 KB	Display	PDB format
PDBx/mmJSON format	9i41.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/i4/9i41 ftp://data.pdbj.org/pub/pdb/validation_reports/i4/9i41	HTTPS FTP

-
Related structure data

Related structure data	9i3wC 9i3xC 9i3zC 9i40C 9i42C 9i43C 9i45C 9i4bC 9i4cC 9i4dC 9i4eC C: citing same article (ref.)

-
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

L: light chain

H: heavy chain

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	77.826, 156.587, 78.461
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	20
Space group name H-M	C222₁

Components on special symmetry positions

ID	Model	Components
1	1	H-441- HOH
2	1	H-517- HOH

#1: Antibody	light chain Mass: 22800.232 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	heavy chain Mass: 25439.330 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-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: C₂H₆O₂ / Feature type: SUBJECT OF INVESTIGATION
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 507 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	Y

-
Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

Crystal	Density Matthews: 2.48 Å³/Da / Density % sol: 50.36 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, sitting drop / Details: 25% (w/v) PEG 3350, 0.1 M bis-Tris, pH 5.5

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 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: 0.9763 Å / Relative weight: 1
Reflection	Resolution: 1.32→78.416 Å / Num. obs: 112322 / % possible obs: 99.9 % / Redundancy: 69.4 % / CC_1/2: 1 / Net I/σ(I): 18.9
Reflection shell	Resolution: 1.32→1.354 Å / Num. unique obs: 5448 / CC_1/2: 0.6

-
Processing

Software

Name	Version	Classification
REFMAC	5.8.0419	refinement
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.32→78.416 Å / Cor.coef. F_o:F_c: 0.979 / Cor.coef. F_o:F_c free: 0.97 / SU B: 1.741 / SU ML: 0.031 / Cross valid method: FREE R-VALUE / ESU R: 0.046 / ESU R Free: 0.046
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.1738	5587	5.036 %
R_work	0.1428	105345	-
all	0.144	-	-
obs	-	110932	98.695 %

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: 19.504 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.296 Å²	0 Å²	-0 Å²
2-	-	0.035 Å²	0 Å²
3-	-	-	0.261 Å²

Refinement step

Cycle: LAST / Resolution: 1.32→78.416 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3271	0	45	507	3823

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.012	3576
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	3277
X-RAY DIFFRACTION	r_angle_refined_deg	1.727	1.797	4910
X-RAY DIFFRACTION	r_angle_other_deg	0.647	1.718	7647
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.16	5	504
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	9.624	5	11
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.229	10	554
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	14.961	10	125
X-RAY DIFFRACTION	r_chiral_restr	0.104	0.2	558
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.02	4247
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	783
X-RAY DIFFRACTION	r_nbd_refined	0.212	0.2	523
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.203	0.2	2894
X-RAY DIFFRACTION	r_nbtor_refined	0.175	0.2	1677
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.091	0.2	1855
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.255	0.2	353
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.092	0.2	2
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.204	0.2	23
X-RAY DIFFRACTION	r_nbd_other	0.167	0.2	108
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.153	0.2	55
X-RAY DIFFRACTION	r_mcbond_it	7.428	1.926	1846
X-RAY DIFFRACTION	r_mcbond_other	7.426	1.926	1846
X-RAY DIFFRACTION	r_mcangle_it	9.956	3.468	2323
X-RAY DIFFRACTION	r_mcangle_other	9.956	3.469	2324
X-RAY DIFFRACTION	r_scbond_it	8.678	2.219	1730
X-RAY DIFFRACTION	r_scbond_other	8.676	2.22	1731
X-RAY DIFFRACTION	r_scangle_it	12.135	3.896	2556
X-RAY DIFFRACTION	r_scangle_other	12.133	3.896	2557
X-RAY DIFFRACTION	r_lrange_it	18.73	22.189	3926
X-RAY DIFFRACTION	r_lrange_other	18.728	22.191	3927
X-RAY DIFFRACTION	r_rigid_bond_restr	4.546	3	6853

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
1.32-1.354	0.381	423	0.353	7336	0.355	8209	0.893	0.906	94.5182	0.345
1.354-1.391	0.335	398	0.303	7395	0.304	8064	0.932	0.939	96.6394	0.285
1.391-1.431	0.313	362	0.252	7204	0.255	7790	0.935	0.959	97.1245	0.226
1.431-1.475	0.253	359	0.21	7055	0.212	7603	0.96	0.972	97.5141	0.182
1.475-1.524	0.225	355	0.17	6892	0.173	7356	0.967	0.982	98.5182	0.144
1.524-1.577	0.187	339	0.138	6704	0.141	7128	0.979	0.988	98.8075	0.117
1.577-1.637	0.169	342	0.12	6500	0.122	6887	0.982	0.991	99.3466	0.102
1.637-1.703	0.171	300	0.117	6294	0.119	6630	0.982	0.991	99.457	0.101
1.703-1.779	0.139	313	0.101	6057	0.103	6397	0.988	0.994	99.5779	0.09
1.779-1.866	0.144	333	0.101	5733	0.104	6082	0.988	0.994	99.7369	0.092
1.866-1.967	0.162	280	0.109	5497	0.112	5782	0.984	0.993	99.9135	0.103
1.967-2.086	0.146	287	0.119	5234	0.12	5523	0.987	0.992	99.9638	0.115
2.086-2.23	0.151	273	0.112	4884	0.114	5158	0.987	0.993	99.9806	0.111
2.23-2.408	0.172	229	0.123	4600	0.125	4831	0.983	0.991	99.9586	0.123
2.408-2.638	0.17	256	0.128	4200	0.131	4456	0.982	0.99	100	0.131
2.638-2.949	0.146	214	0.133	3824	0.133	4038	0.986	0.989	100	0.141
2.949-3.404	0.14	187	0.137	3411	0.137	3598	0.989	0.988	100	0.148
3.404-4.167	0.173	149	0.145	2915	0.147	3064	0.98	0.987	100	0.164
4.167-5.885	0.163	118	0.147	2287	0.148	2405	0.987	0.989	100	0.174
5.885-78.416	0.233	70	0.198	1323	0.2	1398	0.962	0.968	99.6423	0.227

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi