PDB-5i2m: CRYSTAL STRUCTURE OF VSV-INDIANA (MUDD-SUMMERS STRAIN) GLYCOPROTE...

ID or keywords:

Entry

Database: PDB / ID: 5i2m

Title

CRYSTAL STRUCTURE OF VSV-INDIANA (MUDD-SUMMERS STRAIN) GLYCOPROTEIN UNDER ITS ACIDIC CONFORMATION

Components

Glycoprotein G

Keywords

MEMBRANE PROTEIN / MEMBRANE / LIPOPROTEIN / GLYCOPROTEIN / TRANSMEMBRANE / ENVELOPE PROTEIN

Function / homology

Function and homology information

host cell membrane / clathrin-dependent endocytosis of virus by host cell / entry receptor-mediated virion attachment to host cell / fusion of virus membrane with host endosome membrane / viral envelope / virion membrane / membrane
Similarity search - Function

Biological species

Vesicular stomatitis Indiana virus

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SIRAS / Resolution: 2.4 Å

Authors

Roche, S. / Bressanelli, S.

Citation

Journal: Science / Year: 2006
Title: Crystal structure of the low-pH form of the vesicular stomatitis virus glycoprotein G.
Authors: Roche, S. / Bressanelli, S. / Rey, F.A. / Gaudin, Y.

History

Deposition	Feb 9, 2016	Deposition site: RCSB / Processing site: PDBE
Supersession	Feb 24, 2016	ID: 2cmz
Revision 1.0	Feb 24, 2016	Provider: repository / Type: Initial release
Revision 1.1	Nov 20, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_symmetry

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	5i2m.cif.gz	513.4 KB	Display	PDBx/mmCIF format
PDB format	pdb5i2m.ent.gz	426.5 KB	Display	PDB format
PDBx/mmJSON format	5i2m.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/i2/5i2m ftp://data.pdbj.org/pub/pdb/validation_reports/i2/5i2m	HTTPS FTP

-
Related structure data

Similar structure data	4d6w-d 3kz1-d 2fv2-d 3gq9-1 7792 6eyn-d 8966 1f51-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Glycoprotein G

B: Glycoprotein G

C: Glycoprotein G

hetero molecules

144 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by software

Unit cell

Length a, b, c (Å)	71.270, 224.200, 375.740
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	20
Space group name H-M	C222₁

#1: Protein	Glycoprotein G Mass: 47342.039 Da / Num. of mol.: 3 / Source method: isolated from a natural source Source: (natural) Vesicular stomatitis Indiana virus (strain Mudd-Summers) Strain: Mudd-Summers / References: UniProt: P0C2X0
#2: Chemical	ChemComp-PE4 / 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL / POLYETHYLENE GLYCOL PEG4000 Mass: 354.436 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₁₆H₃₄O₈ / Comment: precipitant*YM
#3: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 508 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

-
Experiment

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

-
Sample preparation

Crystal grow	Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 Details: PROTEIN WAS CRYSTALLIZED FROM 28% PEG 400, 200 MM CACL2, 100 MM HEPES, PH 7.0; THEN SOAKED IN 35% PEG 400, 200 MM CACL2, 100 MM HEPES, PH 7.0

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
Detector	Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 4, 2005
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.934 Å / Relative weight: 1
Reflection	Resolution: 2.4→50 Å / Num. obs: 117851 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 5.9 % / R_merge(I) obs: 0.08 / Net I/σ(I): 16
Reflection shell	Resolution: 2.4→2.5 Å / Redundancy: 5.9 % / R_merge(I) obs: 0.55 / Mean I/σ(I) obs: 3.5 / % possible all: 99.4

-
Processing

Software

Name	Version	Classification
PHENIX	1.10.1_2155	refinement
XDS		data reduction
XSCALE		data scaling
SHARP		phasing

Refinement

Method to determine structure:

SIRAS / Resolution: 2.4→24.961 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / Phase error: 20.81

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2149	5887	5 %	Random
R_work	0.1829	-	-	-
obs	0.1845	117755	99.91 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 2.4→24.961 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9700	0	106	508	10314

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	10117
X-RAY DIFFRACTION	f_angle_d	0.956	13747
X-RAY DIFFRACTION	f_dihedral_angle_d	13.493	5985
X-RAY DIFFRACTION	f_chiral_restr	0.056	1444
X-RAY DIFFRACTION	f_plane_restr	0.007	1742

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 (%)
2.4-2.4273	0.3517	188	0.3124	3576	X-RAY DIFFRACTION	98
2.4273-2.4558	0.3038	198	0.2778	3765	X-RAY DIFFRACTION	100
2.4558-2.4858	0.3049	192	0.2718	3634	X-RAY DIFFRACTION	100
2.4858-2.5172	0.3207	192	0.2652	3667	X-RAY DIFFRACTION	100
2.5172-2.5503	0.2877	198	0.2507	3764	X-RAY DIFFRACTION	100
2.5503-2.5852	0.2438	192	0.2406	3643	X-RAY DIFFRACTION	100
2.5852-2.6221	0.2575	196	0.2289	3740	X-RAY DIFFRACTION	100
2.6221-2.6612	0.2571	194	0.2307	3675	X-RAY DIFFRACTION	100
2.6612-2.7027	0.3117	194	0.2305	3681	X-RAY DIFFRACTION	100
2.7027-2.747	0.2679	197	0.2172	3741	X-RAY DIFFRACTION	100
2.747-2.7943	0.2664	193	0.2201	3679	X-RAY DIFFRACTION	100
2.7943-2.845	0.2468	196	0.2129	3718	X-RAY DIFFRACTION	100
2.845-2.8996	0.2651	191	0.2171	3641	X-RAY DIFFRACTION	100
2.8996-2.9587	0.2395	199	0.2124	3770	X-RAY DIFFRACTION	100
2.9587-3.023	0.2344	194	0.211	3685	X-RAY DIFFRACTION	100
3.023-3.0932	0.2338	198	0.2042	3760	X-RAY DIFFRACTION	100
3.0932-3.1704	0.2417	193	0.2031	3673	X-RAY DIFFRACTION	100
3.1704-3.2559	0.2295	197	0.1936	3736	X-RAY DIFFRACTION	100
3.2559-3.3515	0.2078	195	0.1878	3721	X-RAY DIFFRACTION	100
3.3515-3.4594	0.2016	197	0.1852	3728	X-RAY DIFFRACTION	100
3.4594-3.5827	0.2168	196	0.184	3737	X-RAY DIFFRACTION	100
3.5827-3.7257	0.2108	196	0.1729	3713	X-RAY DIFFRACTION	100
3.7257-3.8947	0.1803	197	0.1561	3743	X-RAY DIFFRACTION	100
3.8947-4.0992	0.1861	197	0.1578	3740	X-RAY DIFFRACTION	100
4.0992-4.3547	0.1721	198	0.1448	3765	X-RAY DIFFRACTION	100
4.3547-4.6889	0.1694	199	0.1402	3788	X-RAY DIFFRACTION	100
4.6889-5.157	0.2002	199	0.1472	3784	X-RAY DIFFRACTION	100
5.157-5.8947	0.1942	201	0.1596	3803	X-RAY DIFFRACTION	100
5.8947-7.3945	0.214	201	0.1724	3834	X-RAY DIFFRACTION	100
7.3945-24.9619	0.179	209	0.1704	3964	X-RAY DIFFRACTION	100

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	4.2114	0.7676	-0.0086	3.4788	-0.0123	4.0167	-0.1361	-0.2927	0.661	0.2535	0.1764	-0.1468	-0.8372	0.0305	-0.1435	0.4975	0.0425	-0.0412	0.2186	-0.0944	0.6001	19.2078	53.0763	18.2017
2	2.3887	0.5437	0.2171	1.715	0.2622	2.8562	-0.1981	0.1311	0.1014	0.0029	0.0737	0.3091	-0.0365	-0.4904	0.1411	0.2206	0.0442	-0.0213	0.3093	-0.0035	0.4473	14.7622	36.499	9.1071
3	3.1228	2.2018	1.4789	4.8023	0.3728	7.6652	-0.1642	0.3938	0.2493	-0.3248	0.2288	0.4738	-0.4938	0.5222	0.0325	0.2632	0.0013	-0.0595	0.6575	-0.0392	0.5421	-4.8688	29.7116	-6.3004
4	0.5639	-0.5242	-0.2306	-0.496	0.1729	7.8927	0.0548	-0.2128	-0.0517	-0.3237	0.0301	0.2293	-0.4949	-0.6932	-0.1361	1.2262	-0.1547	-0.2231	0.9997	0.0328	0.5266	-1.7003	30.9408	-50.6101
5	2.345	-1.0589	-0.8172	3.9145	0.6717	3.3142	-0.0945	-0.1402	-0.2477	0.1045	0.2099	-0.384	0.1628	0.4334	-0.11	0.2166	0.0083	-0.0477	0.4126	-0.0181	0.5587	47.5249	22.99	12.8424
6	1.4154	0.2865	0.8522	2.2935	-0.2162	2.2013	-0.2224	0.232	0.1395	-0.1198	0.1063	-0.1457	-0.2062	0.3962	0.1147	0.2234	-0.037	-0.0042	0.3572	0.0167	0.4549	33.2977	34.0122	4.8333
7	1.7688	0.6179	-0.6027	3.3703	0.603	2.2475	-0.1382	0.351	0.0408	-0.773	0.4324	0.2763	0.3783	-0.5334	-0.1082	0.7573	-0.3765	-0.1636	0.6668	0.1167	0.5422	31.7766	50.6228	-14.6735
8	1.543	0.1803	1.4876	0.0235	0.6238	4.7331	0.0588	-0.0346	0.0967	-0.1061	-0.0872	-0.0736	-0.9608	0.4232	0.0689	1.5706	-0.4025	-0.2718	0.8802	0.0344	0.5809	17.4987	38.8286	-55.1129
9	5.3411	-0.1681	0.236	2.6732	-0.3302	3.8192	-0.0053	-0.222	-0.2925	0.3155	0.2088	0.6885	0.5085	-0.917	0.0335	0.3577	-0.0654	0.1461	0.4714	0.1303	0.5358	8.9598	12.9535	20.8641
10	1.0088	-0.6237	0.1827	1.8983	-0.1235	5.7944	-0.0676	-0.0113	-0.0548	-0.1089	-0.0246	0.0175	0.2902	0.0752	0.0447	0.2472	-0.0223	0.0467	0.2524	0.0331	0.4452	22.1416	19.3618	8.3333
11	4.665	0.3064	2.21	2.3172	0.4334	4.4357	0.0862	0.3652	-0.0868	-0.4845	0.1085	-0.136	-0.5799	0.2705	-0.1818	0.5017	-0.0004	0.066	0.2594	0.0101	0.3763	31.1691	8.208	-13.7643
12	0.1178	-0.266	1.4859	0.4962	-0.4936	6.7644	0.0312	0.2914	-0.1445	-0.1792	0.0443	0.0416	0.2566	0.472	-0.116	1.2528	-0.0667	-0.2401	0.7925	0.0573	0.511	14.7112	18.2508	-54.3277

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resseq 1:17) or (chain A and resseq 310:383)
2	X-RAY DIFFRACTION	2	(chain A and resseq 18:35) or (chain A and resseq 259:309) or (chain A and resseq 384:410)
3	X-RAY DIFFRACTION	3	(chain A and resseq 36:48) or (chain A and resseq 181:258) or (chain A and resseq 1410:1410)
4	X-RAY DIFFRACTION	4	(chain A and resseq 49:180)
5	X-RAY DIFFRACTION	5	(chain B and resseq 1:17) or (chain B and resseq 310:383) or (chain B and resseq 1412:1412) or (chain B and resseq 1413:1413)
6	X-RAY DIFFRACTION	6	(chain B and resseq 18:35) or (chain B and resseq 259:309) or (chain B and resseq 384:410)
7	X-RAY DIFFRACTION	7	(chain B and resseq 36:48) or (chain B and resseq 181:258) or (chain B and resseq 1411:1411)
8	X-RAY DIFFRACTION	8	(chain B and resseq 49:180)
9	X-RAY DIFFRACTION	9	(chain C and resseq 1:17) or (chain C and resseq 310:383)
10	X-RAY DIFFRACTION	10	(chain C and resseq 18:35) or (chain C and resseq 259:309) or (chain C and resseq 384:410)
11	X-RAY DIFFRACTION	11	(chain C and resseq 36:48) or (chain C and resseq 181:258) or (chain C and resseq 1409:1409)
12	X-RAY DIFFRACTION	12	(chain C and resseq 49:180)

-
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