PDB-9fs7: Coxsackievirus A16 3C protease in C2 2 21 spacegroup

ID or keywords:

Entry

Database: PDB / ID: 9fs7

Title

Coxsackievirus A16 3C protease in C2 2 21 spacegroup

Components

Genome polyprotein

Keywords

HYDROLASE / 3C protease Coxackie virus virus A clade

Function / homology

Function and homology information

T=pseudo3 icosahedral viral capsid / host cell cytoplasm / cysteine-type endopeptidase activity / symbiont entry into host cell / virion attachment to host cell / proteolysis / cytoplasm
Similarity search - Function

Biological species

Coxsackievirus A16

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.37 Å

Authors

Fairhead, M. / Lithgo, R. / MacLean, M. / Bowesman-Jones, H. / Aschenbrenner, J.C. / Balcomb, B.H. / Capkin, E. / Chandran, A.V. / Godoy, A.S. / Marples, P.G. ...

Funding support

United States, 1items

Citation

Journal: To Be Published
Title: Coxsackievirus A16 3C protease in C2 2 21 spacegroup
Authors: Fairhead, M. / Lithgo, R. / MacLean, M. / Bowesman-Jones, H. / Aschenbrenner, J.C. / Balcomb, B.H. / Capkin, E. / Chandran, A.V. / Godoy, A.S. / Marples, P.G. / Fearon, D. / von Delft, F. / Koekemoer, L.

History

Deposition	Jun 20, 2024	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jul 10, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	9fs7.cif.gz	190.2 KB	Display	PDBx/mmCIF format
PDB format	pdb9fs7.ent.gz	124.1 KB	Display	PDB format
PDBx/mmJSON format	9fs7.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	9fs7_validation.pdf.gz	419.1 KB	Display	wwPDB validaton report
Full document	9fs7_full_validation.pdf.gz	419.3 KB	Display
Data in XML	9fs7_validation.xml.gz	10.5 KB	Display
Data in CIF	9fs7_validation.cif.gz	15 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/fs/9fs7 ftp://data.pdbj.org/pub/pdb/validation_reports/fs/9fs7	HTTPS FTP

-
Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#20 - Aug 2001 Poliovirus and Rhinovirus similarity (4) #200 - Aug 2016 Quasisymmetry in Icosahedral Viruses similarity (1)

Deposited unit

A: Genome polyprotein

20.1 kDa, 1 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)	64.36, 65.17, 76.09
Angle α, β, γ (deg.)	90, 90, 90
Int Tables number	20
Space group name H-M	C222₁

Components on special symmetry positions

ID	Model	Components
1	1	A-280- HOH
2	1	A-337- HOH

#1: Protein	Genome polyprotein Mass: 20130.109 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Coxsackievirus A16 / Production host: Escherichia coli (E. coli) / References: UniProt: E5L254
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 174 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 1.98 Å³/Da / Density % sol: 37.93 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop Details: Shotgun1 well A01 0.2M Magnesium chloride hexahydrate, 0.1M Tris pH 8.5, 30% w/v PEG 4000,

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9212 Å
Detector	Type: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Dec 12, 2023
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9212 Å / Relative weight: 1
Reflection	Resolution: 1.37→39.24 Å / Num. obs: 25094 / % possible obs: 73.91 % / Redundancy: 10.5 % / CC_1/2: 0.999 / Net I/σ(I): 20.2
Reflection shell	Resolution: 1.37→1.39 Å / Num. unique obs: 323 / CC_1/2: 0.264

-
Processing

Software

Name	Version	Classification
REFMAC	5.8.0425	refinement
xia2		data reduction
xia2		data scaling
REFMAC		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.37→39.236 Å / Cor.coef. F_o:F_c: 0.974 / Cor.coef. F_o:F_c free: 0.958 / SU B: 3.33 / SU ML: 0.056 / Cross valid method: FREE R-VALUE / ESU R: 0.097 / ESU R Free: 0.083
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2065	1339	5.341 %
R_work	0.1511	23729	-
all	0.154	-	-
obs	-	25068	73.829 %

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: 23.874 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.273 Å²	-0 Å²	-0 Å²
2-	-	1.028 Å²	0 Å²
3-	-	-	-0.756 Å²

Refinement step

Cycle: LAST / Resolution: 1.37→39.236 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1391	0	0	174	1565

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.012	1457
X-RAY DIFFRACTION	r_bond_other_d	0.003	0.016	1410
X-RAY DIFFRACTION	r_angle_refined_deg	1.815	1.819	1978
X-RAY DIFFRACTION	r_angle_other_deg	0.77	1.752	3233
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.711	5	187
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	8.95	5	11
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.48	10	248
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	15.631	10	64
X-RAY DIFFRACTION	r_chiral_restr	0.099	0.2	227
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	1747
X-RAY DIFFRACTION	r_gen_planes_other	0.003	0.02	343
X-RAY DIFFRACTION	r_nbd_refined	0.194	0.2	217
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.163	0.2	1210
X-RAY DIFFRACTION	r_nbtor_refined	0.157	0.2	688
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.077	0.2	744
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.174	0.2	102
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.194	0.2	15
X-RAY DIFFRACTION	r_nbd_other	0.161	0.2	68
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.372	0.2	22
X-RAY DIFFRACTION	r_mcbond_it	6.218	2.163	742
X-RAY DIFFRACTION	r_mcbond_other	6.173	2.162	742
X-RAY DIFFRACTION	r_mcangle_it	8.872	3.899	931
X-RAY DIFFRACTION	r_mcangle_other	8.874	3.904	932
X-RAY DIFFRACTION	r_scbond_it	7.883	2.455	715
X-RAY DIFFRACTION	r_scbond_other	7.878	2.459	716
X-RAY DIFFRACTION	r_scangle_it	11.227	4.376	1047
X-RAY DIFFRACTION	r_scangle_other	11.222	4.38	1048
X-RAY DIFFRACTION	r_lrange_it	16.689	29.048	1544
X-RAY DIFFRACTION	r_lrange_other	15.125	26.782	1491
X-RAY DIFFRACTION	r_rigid_bond_restr	3.891	3	2867

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
1.37-1.406	0.511	16	0.386	487	0.39	2463	0.906	0.912	20.4223	0.39
1.406-1.444	0.338	38	0.342	617	0.342	2414	0.938	0.937	27.1334	0.339
1.444-1.486	0.295	30	0.288	766	0.288	2359	0.955	0.959	33.7431	0.27
1.486-1.532	0.336	60	0.264	926	0.268	2306	0.939	0.97	42.758	0.235
1.532-1.582	0.324	59	0.228	1112	0.233	2207	0.973	0.977	53.0585	0.201
1.582-1.637	0.242	82	0.199	1354	0.201	2152	0.961	0.982	66.7286	0.169
1.637-1.699	0.2	102	0.146	1715	0.149	2075	0.978	0.988	87.5663	0.12
1.699-1.768	0.245	82	0.136	1807	0.14	1982	0.963	0.989	95.3078	0.117
1.768-1.847	0.232	101	0.128	1787	0.133	1927	0.965	0.99	97.9761	0.112
1.847-1.936	0.205	113	0.124	1686	0.128	1828	0.975	0.991	98.4136	0.113
1.936-2.041	0.212	76	0.131	1645	0.135	1748	0.973	0.99	98.4554	0.125
2.041-2.164	0.199	80	0.134	1565	0.137	1669	0.976	0.99	98.562	0.132
2.164-2.313	0.2	99	0.137	1448	0.141	1565	0.975	0.989	98.8498	0.138
2.313-2.498	0.18	75	0.131	1367	0.134	1455	0.98	0.99	99.1065	0.133
2.498-2.735	0.201	82	0.133	1262	0.137	1352	0.971	0.989	99.4083	0.141
2.735-3.056	0.185	62	0.145	1173	0.146	1242	0.984	0.987	99.4364	0.157
3.056-3.525	0.185	55	0.149	1027	0.151	1087	0.978	0.986	99.54	0.169
3.525-4.309	0.185	48	0.136	878	0.139	929	0.979	0.989	99.6771	0.163
4.309-6.057	0.179	43	0.174	696	0.174	742	0.982	0.986	99.5957	0.22
6.057-39.236	0.28	36	0.233	411	0.237	451	0.966	0.966	99.1131	0.296

-
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