PDB-8a2e: Crystal Structure of Human Parechovirus 3 2A protein

ID or keywords:

Entry

Database: PDB / ID: 8a2e

Title

Crystal Structure of Human Parechovirus 3 2A protein

Components

2A protein

Keywords

VIRAL PROTEIN / 2A protein / unknown function / NlpC/P60 protein

Function / homology

Function and homology information

RNA-protein covalent cross-linking / : / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / protein complex oligomerization / monoatomic ion channel activity / RNA helicase activity / symbiont entry into host cell / viral RNA genome replication ...
Similarity search - Function

Biological species

Human parechovirus 3

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.29 Å

Authors

von Castelmur, E. / Zhu, L. / wang, X. / Fry, E. / Ren, J. / Perrakis, A. / Stuart, D.I.

Funding support

United Kingdom, 1items

Citation

Journal: To Be Published
Title: Structural plasticity of 2A proteins in the Parechovirus family.
Authors: von Castelmur, E. / Perrakis, A.

History

Deposition	Jun 3, 2022	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jun 14, 2023	Provider: repository / Type: Initial release
Revision 1.1	Feb 7, 2024	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2	Feb 14, 2024	Group: Database references / Category: citation / Item: _citation.title

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	8a2e.cif.gz	429.1 KB	Display	PDBx/mmCIF format
PDB format	pdb8a2e.ent.gz		Display	PDB format
PDBx/mmJSON format	8a2e.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	8a2e_validation.pdf.gz	520.8 KB	Display	wwPDB validaton report
Full document	8a2e_full_validation.pdf.gz	529.9 KB	Display
Data in XML	8a2e_validation.xml.gz	39.5 KB	Display
Data in CIF	8a2e_validation.cif.gz	52.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/a2/8a2e ftp://data.pdbj.org/pub/pdb/validation_reports/a2/8a2e	HTTPS FTP

-
Related structure data

Related structure data	7ztwS S: Starting model for refinement
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 (10) #200 - Aug 2016 Quasisymmetry in Icosahedral Viruses similarity (1)

Deposited unit

AAA: 2A protein

BBB: 2A protein

CCC: 2A protein

DDD: 2A protein

EEE: 2A protein

FFF: 2A protein

GGG: 2A protein

HHH: 2A protein

hetero molecules

144 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

AAA: 2A protein

BBB: 2A protein

CCC: 2A protein

DDD: 2A protein

hetero molecules

defined by author&software
72.3 kDa, 4 polymers

2

EEE: 2A protein

FFF: 2A protein

GGG: 2A protein

HHH: 2A protein

hetero molecules

defined by author&software
72.2 kDa, 4 polymers

Unit cell

Length a, b, c (Å)	141.680, 141.680, 183.880
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	146
Space group name H-M	H3

Components on special symmetry positions

ID	Model	Components
1	1	HHH-301- HOH

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	AAA
2	1	CCC
3	1	EEE
4	1	GGG
5	2	BBB
6	2	DDD
7	2	FFF
8	2	HHH

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	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	MET	MET	GLY	GLY	AAA	A	0 - 147	1 - 148
2	1	1	MET	MET	GLY	GLY	CCC	C	0 - 147	1 - 148
3	1	1	MET	MET	GLY	GLY	EEE	E	0 - 147	1 - 148
4	1	1	MET	MET	GLY	GLY	GGG	G	0 - 147	1 - 148
5	2	2	MET	MET	SER	SER	BBB	B	12 - 88	13 - 89
5	3	2	ASN	ASN	HIS	HIS	BBB	B	107 - 143	108 - 144
6	2	2	MET	MET	SER	SER	DDD	D	12 - 88	13 - 89
6	3	2	ASN	ASN	HIS	HIS	DDD	D	107 - 143	108 - 144
7	2	2	MET	MET	SER	SER	FFF	F	12 - 88	13 - 89
7	3	2	ASN	ASN	HIS	HIS	FFF	F	107 - 143	108 - 144
8	2	2	MET	MET	SER	SER	HHH	H	12 - 88	13 - 89
8	3	2	ASN	ASN	HIS	HIS	HHH	H	107 - 143	108 - 144

NCS ensembles :

ID	Details
1	Global NCS restraints between domains: 1 2 3 4
2	Global NCS restraints between domains: 5 6 7 8

#1: Protein	2A protein Mass: 17906.180 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human parechovirus 3 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: U3KRG6
#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 37 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.48 Å³/Da / Density % sol: 50.39 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 1.7 M Ammonium sulphate, 0.05 M Sodium Cacodylate pH 6.5

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 17, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97625 Å / Relative weight: 1
Reflection	Resolution: 2.29→102 Å / Num. obs: 61983 / % possible obs: 100 % / Redundancy: 10.2 % / CC_1/2: 1 / R_rim(I) all: 0.11 / Net I/σ(I): 22.86
Reflection shell	Resolution: 2.29→2.34 Å / Num. unique obs: 4602 / CC_1/2: 0.59 / R_rim(I) all: 1.117

-
Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
xia2		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 7ZTW

7ztw

Resolution: 2.29→73.576 Å / Cor.coef. F_o:F_c: 0.971 / Cor.coef. F_o:F_c free: 0.958 / SU B: 10.208 / SU ML: 0.12 / Cross valid method: THROUGHOUT / ESU R: 0.056 / ESU R Free: 0.042
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2144	3220	5.196 %
R_work	0.1783	58751	-
all	0.18	-	-
obs	-	61971	99.971 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 75.014 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	3.792 Å²	0 Å²	0 Å²
2-	-	3.792 Å²	0 Å²
3-	-	-	-7.584 Å²

Refinement step

Cycle: LAST / Resolution: 2.29→73.576 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9030	0	70	37	9137

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.006	0.013	9291
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.015	8622
X-RAY DIFFRACTION	r_angle_refined_deg	1.318	1.641	12584
X-RAY DIFFRACTION	r_angle_other_deg	1.226	1.577	19864
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.875	5	1131
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	32.019	23.08	461
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.101	15	1579
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.586	15	37
X-RAY DIFFRACTION	r_chiral_restr	0.054	0.2	1264
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	10361
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	2113
X-RAY DIFFRACTION	r_nbd_refined	0.199	0.2	1740
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.179	0.2	7958
X-RAY DIFFRACTION	r_nbtor_refined	0.162	0.2	4561
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.079	0.2	4133
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.149	0.2	215
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.05	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.149	0.2	23
X-RAY DIFFRACTION	r_nbd_other	0.247	0.2	125
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.168	0.2	11
X-RAY DIFFRACTION	r_mcbond_it	3.163	6.214	4542
X-RAY DIFFRACTION	r_mcbond_other	3.163	6.213	4541
X-RAY DIFFRACTION	r_mcangle_it	4.684	9.313	5664
X-RAY DIFFRACTION	r_mcangle_other	4.684	9.314	5665
X-RAY DIFFRACTION	r_scbond_it	3.504	6.619	4749
X-RAY DIFFRACTION	r_scbond_other	3.461	6.571	4718
X-RAY DIFFRACTION	r_scangle_it	5.299	9.774	6919
X-RAY DIFFRACTION	r_scangle_other	5.262	9.7	6872
X-RAY DIFFRACTION	r_lrange_it	8.018	72.532	10012
X-RAY DIFFRACTION	r_lrange_other	8.017	72.523	10012

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: medium positional; mediume thermal / Weight B_iso : 2 / Weight position: 0.5

Ens-ID	Dom-ID	Auth asym-ID	Rms dev B_iso (Å²)	Rms dev position (Å)
1	1	AAA	6.0085	1.85383
1	2	CCC	6.52208	1.84531
1	3	EEE	5.40709	1.85669
1	4	FFF	12.86977	5.40586
2	5	BBB	9.22707	0.46312
2	6	DDD	3.52693	0.5137
2	7	FFF	4.35104	0.43587
2	8	HHH	8.673	0.49304

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.29-2.349	0.303	248	0.23	4338	X-RAY DIFFRACTION	99.6956
2.349-2.414	0.303	229	0.222	4263	X-RAY DIFFRACTION	99.9555
2.414-2.484	0.285	188	0.221	4140	X-RAY DIFFRACTION	100
2.484-2.56	0.272	210	0.212	4005	X-RAY DIFFRACTION	100
2.56-2.644	0.282	181	0.214	3908	X-RAY DIFFRACTION	100
2.644-2.737	0.235	190	0.208	3761	X-RAY DIFFRACTION	100
2.737-2.84	0.27	215	0.216	3638	X-RAY DIFFRACTION	100
2.84-2.956	0.234	194	0.217	3446	X-RAY DIFFRACTION	100
2.956-3.087	0.262	211	0.224	3307	X-RAY DIFFRACTION	100
3.087-3.238	0.237	213	0.207	3157	X-RAY DIFFRACTION	100
3.238-3.413	0.238	191	0.208	3021	X-RAY DIFFRACTION	100
3.413-3.619	0.243	143	0.196	2879	X-RAY DIFFRACTION	100
3.619-3.869	0.192	109	0.173	2729	X-RAY DIFFRACTION	100
3.869-4.178	0.173	123	0.161	2519	X-RAY DIFFRACTION	100
4.178-4.576	0.183	113	0.148	2341	X-RAY DIFFRACTION	100
4.576-5.115	0.207	126	0.145	2093	X-RAY DIFFRACTION	100
5.115-5.904	0.196	108	0.159	1828	X-RAY DIFFRACTION	100
5.904-7.225	0.172	99	0.173	1538	X-RAY DIFFRACTION	100
7.225-10.192	0.175	77	0.139	1194	X-RAY DIFFRACTION	100
10.192-73.576	0.232	52	0.188	646	X-RAY DIFFRACTION	99.7143

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	0.313	-0.0722	0.4637	0.5306	0.4764	1.8817	0.0884	-0.1041	-0.1228	0.1413	-0.0502	0.0215	0.1907	-0.1893	-0.0382	0.1079	-0.0768	-0.05	0.1475	0.0686	0.131	31.8975	-10.2595	24.198
2	1.531	0.9064	-0.3449	1.8934	-0.3426	1.1577	0.038	0.1197	-0.2666	-0.0625	-0.0131	-0.0976	0.1506	-0.1709	-0.0248	0.0318	-0.0264	-0.0292	0.0891	-0.0062	0.0879	22.3093	-15.5656	0.2781
3	0.7438	0.4446	0.2076	0.956	0.3892	1.6927	0.0386	-0.0205	0.0272	-0.0347	-0.0736	-0.0617	-0.2243	-0.0992	0.035	0.0441	0.0274	0.0186	0.0648	0.0162	0.0699	33.9611	14.0076	1.9877
4	1.7845	0.4689	0.5864	3.0537	-1.4349	2.3473	0.0269	-0.4075	0.3492	0.5928	-0.0101	0.2692	-0.6845	-0.4305	-0.0168	0.232	0.0809	0.0557	0.1956	-0.0832	0.0875	25.833	20.7068	26.318
5	0.4037	0.2939	0.2837	0.4713	-0.1652	2.6037	0.0005	-0.0597	0.0437	-0.0848	0.0231	0.05	0.0469	-0.3756	-0.0236	0.0707	0.0331	0.0297	0.1259	0.0004	0.1199	29.52	7.3147	-37.6586
6	2.6434	0.2417	-0.2557	1.3589	-0.0381	3.2567	0.0705	0.2574	0.0934	-0.2177	0.0777	0.2596	-0.169	-0.9545	-0.1482	0.1512	0.0971	-0.0354	0.3363	0.0945	0.1447	21.2472	13.0785	-62.0832
7	0.6533	0.2088	0.2268	0.1371	0.2028	2.2276	0.0249	0.002	0.1755	-0.0512	0.052	0.0003	-0.4026	0.1594	-0.077	0.1807	-0.0173	0.0698	0.0518	-0.0175	0.1778	52.4373	17.4521	-59.0352
8	2.0861	0.0314	-0.5418	1.617	0.0781	3.1826	0.2484	-0.38	0.4123	-0.0038	0.1026	-0.2737	-0.9243	0.5651	-0.3511	0.3121	-0.161	0.1279	0.1837	-0.1774	0.2425	53.154	27.5123	-34.7838

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	AAA	0 - 147
2	X-RAY DIFFRACTION	2	ALL	BBB	11 - 146
3	X-RAY DIFFRACTION	3	ALL	CCC	0 - 147
4	X-RAY DIFFRACTION	4	ALL	DDD	11 - 147
5	X-RAY DIFFRACTION	5	ALL	EEE	0 - 147
6	X-RAY DIFFRACTION	6	ALL	FFF	11 - 146
7	X-RAY DIFFRACTION	7	ALL	GGG	0 - 147
8	X-RAY DIFFRACTION	8	ALL	HHH	11 - 146

-
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://pdbjlvh1.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