PDB-4v5t: X-ray structure of the Grapevine Fanleaf virus

ID or keywords:

Entry

Database: PDB / ID: 4v5t

Title

X-ray structure of the Grapevine Fanleaf virus

Components

COAT PROTEIN

Keywords

VIRUS / FANLEAF DISEASE

Function / homology

Function and homology information

transport of virus in host, cell to cell / host cell plasmodesma / viral capsid / host cell cytoplasm / host cell nucleus / structural molecule activity
Similarity search - Function

Biological species

GRAPEVINE FANLEAF VIRUS

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3 Å

Authors

Schellenberger, P. / Sauter, C. / Lorber, B. / Bron, P. / Trapani, S. / Bergdoll, M. / Marmonier, A. / Schmitt-Keichinger, C. / Lemaire, O. / Demangeat, G. / Ritzenthaler, C.

Citation

Journal: Plos Pathog. / Year: 2011
Title: Structural Insights Into Viral Determinants of Nematode Mediated Grapevine Fanleaf Virus Transmission.
Authors: Schellenberger, P. / Sauter, C. / Lorber, B. / Bron, P. / Trapani, S. / Bergdoll, M. / Marmonier, A. / Schmitt-Keichinger, C. / Lemaire, O. / Demangeat, G. / Ritzenthaler, C.

History

Deposition	Feb 1, 2011	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jul 9, 2014	Provider: repository / Type: Initial release
Supersession	Dec 10, 2014	ID: 2Y7T, 2Y7U, 2Y7V
Revision 1.1	Dec 10, 2014	Group: Other
Revision 1.2	Mar 6, 2019	Group: Data collection / Experimental preparation / Other Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status Item: _exptl_crystal_grow.temp / _pdbx_database_status.date_author_approval / _pdbx_database_status.recvd_author_approval
Revision 1.3	May 8, 2019	Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 1.4	Jan 10, 2024	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4v5t.cif.gz	5.4 MB	Display	PDBx/mmCIF format
PDB format	pdb4v5t.ent.gz		Display	PDB format
PDBx/mmJSON format	4v5t.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4v5t_validation.pdf.gz	818.7 KB	Display	wwPDB validaton report
Full document	4v5t_full_validation.pdf.gz	1.3 MB	Display
Data in XML	4v5t_validation.xml.gz	960.7 KB	Display
Data in CIF	4v5t_validation.cif.gz	1.3 MB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/v5/4v5t ftp://data.pdbj.org/pub/pdb/validation_reports/v5/4v5t	HTTPS FTP

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Related structure data

Related structure data	2y26SC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	2y26-1 5fmo-1 6qcc-1 4v5w-d 6jjc-1 1pgw-1 1ny7-1 2bfu-1 1bmv-1 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

AA: COAT PROTEIN

AB: COAT PROTEIN

AC: COAT PROTEIN

AD: COAT PROTEIN

AE: COAT PROTEIN

AF: COAT PROTEIN

AG: COAT PROTEIN

AH: COAT PROTEIN

AI: COAT PROTEIN

AJ: COAT PROTEIN

AK: COAT PROTEIN

AL: COAT PROTEIN

AM: COAT PROTEIN

AN: COAT PROTEIN

AO: COAT PROTEIN

AP: COAT PROTEIN

AQ: COAT PROTEIN

AR: COAT PROTEIN

AS: COAT PROTEIN

AT: COAT PROTEIN

BA: COAT PROTEIN

BB: COAT PROTEIN

BC: COAT PROTEIN

BD: COAT PROTEIN

BE: COAT PROTEIN

BF: COAT PROTEIN

BG: COAT PROTEIN

BH: COAT PROTEIN

BI: COAT PROTEIN

BJ: COAT PROTEIN

BK: COAT PROTEIN

BL: COAT PROTEIN

BM: COAT PROTEIN

BN: COAT PROTEIN

BO: COAT PROTEIN

BP: COAT PROTEIN

BQ: COAT PROTEIN

BR: COAT PROTEIN

BS: COAT PROTEIN

BT: COAT PROTEIN

CA: COAT PROTEIN

CB: COAT PROTEIN

CC: COAT PROTEIN

CD: COAT PROTEIN

CE: COAT PROTEIN

CF: COAT PROTEIN

CG: COAT PROTEIN

CH: COAT PROTEIN

CI: COAT PROTEIN

CJ: COAT PROTEIN

CK: COAT PROTEIN

CL: COAT PROTEIN

CM: COAT PROTEIN

CN: COAT PROTEIN

CO: COAT PROTEIN

CP: COAT PROTEIN

CQ: COAT PROTEIN

CR: COAT PROTEIN

CS: COAT PROTEIN

CT: COAT PROTEIN

3.36 MDa, 60 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	279.400, 279.600, 293.300
Angle α, β, γ (deg.)	102.40, 116.40, 108.20
Int Tables number	1
Space group name H-M	P1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

#1: Protein	... COAT PROTEIN / 2C-CP Mass: 56073.141 Da / Num. of mol.: 60 / Source method: isolated from a natural source / Source: (natural) GRAPEVINE FANLEAF VIRUS / Strain: GFLV-F13 / References: UniProt: P18474

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 5.27 Å³/Da / Density % sol: 76.66 % / Description: NONE
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: CRYSTALS OF GFLV-F13 WERE GROWN AT 293K BY VAPOR DIFFUSION (1 MICROLITER SITTING DROPS) WITH A VIRUS SOLUTION AT 2.2 MG/ML AND A RESERVOIR CONTAINING 4% (M/V) PEG 3350, 0.1 M HEPES NA PH 7.5 ...Details: CRYSTALS OF GFLV-F13 WERE GROWN AT 293K BY VAPOR DIFFUSION (1 MICROLITER SITTING DROPS) WITH A VIRUS SOLUTION AT 2.2 MG/ML AND A RESERVOIR CONTAINING 4% (M/V) PEG 3350, 0.1 M HEPES NA PH 7.5 AND 0.2% (M/V) AGAROSE.

Crystal

Density Matthews: 5.27 Å³/Da / Density % sol: 76.66 % / Description: NONE

Crystal grow

Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: CRYSTALS OF GFLV-F13 WERE GROWN AT 293K BY VAPOR DIFFUSION (1 MICROLITER SITTING DROPS) WITH A VIRUS SOLUTION AT 2.2 MG/ML AND A RESERVOIR CONTAINING 4% (M/V) PEG 3350, 0.1 M HEPES NA PH 7.5 ...

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.98
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 24, 2009
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.98 Å / Relative weight: 1
Reflection	Resolution: 3→135.426 Å / Num. obs: 1214112 / % possible obs: 88.1 % / Observed criterion σ(I): 0 / Redundancy: 2 % / B_iso Wilson estimate: 36.31 Å² / R_merge(I) obs: 0.1 / Net I/σ(I): 9.2
Reflection shell	Resolution: 3→3.08 Å / Redundancy: 2 % / R_merge(I) obs: 0.36 / Mean I/σ(I) obs: 2.5 / % possible all: 71.7

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Processing

Software

Name	Version	Classification
AMoRE		model building
PHENIX	(PHENIX.REFINE)	refinement
XDS		data reduction
XSCALE		data scaling
AMoRE		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2Y26

2y26

Resolution: 3→135.426 Å / SU ML: 0.32 / σ(F): 0 / Phase error: 19.44 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2073	60925	5 %
R_work	0.1902	-	-
obs	0.1911	1214112	88.26 %

Solvent computation

Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 5.791 Å² / k_sol: 0.332 e/Å³

Displacement parameters

B_iso mean: 36.27 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.628 Å²	-0.5939 Å²	2.5481 Å²
2-	-	-5.1409 Å²	5.1099 Å²
3-	-	-	5.5261 Å²

Refinement step

Cycle: LAST / Resolution: 3→135.426 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	79020	0	0	0	79020

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	243480
X-RAY DIFFRACTION	f_angle_d	1.195	331140
X-RAY DIFFRACTION	f_dihedral_angle_d	14.539	86520
X-RAY DIFFRACTION	f_chiral_restr	0.077	36900
X-RAY DIFFRACTION	f_plane_restr	0.005	42060

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Type	Rms dev position (Å)
1	1	AA	3951	X-RAY DIFFRACTION	POSITIONAL
1	2	AB	3951	X-RAY DIFFRACTION	POSITIONAL	0.081
1	3	AC	3951	X-RAY DIFFRACTION	POSITIONAL	0.083
1	4	AD	3951	X-RAY DIFFRACTION	POSITIONAL	0.089
1	5	AE	3951	X-RAY DIFFRACTION	POSITIONAL	0.089
1	6	AF	3951	X-RAY DIFFRACTION	POSITIONAL	0.079
1	7	AG	3951	X-RAY DIFFRACTION	POSITIONAL	0.09
1	8	AH	3951	X-RAY DIFFRACTION	POSITIONAL	0.104
1	9	AI	3951	X-RAY DIFFRACTION	POSITIONAL	0.09
1	10	AJ	3951	X-RAY DIFFRACTION	POSITIONAL	0.107
1	11	AK	3951	X-RAY DIFFRACTION	POSITIONAL	0.108
1	12	AL	3951	X-RAY DIFFRACTION	POSITIONAL	0.29
1	13	AM	3951	X-RAY DIFFRACTION	POSITIONAL	0.09
1	14	AN	3951	X-RAY DIFFRACTION	POSITIONAL	0.105
1	15	AO	3951	X-RAY DIFFRACTION	POSITIONAL	0.122
1	16	AP	3951	X-RAY DIFFRACTION	POSITIONAL	0.245
1	17	AQ	3951	X-RAY DIFFRACTION	POSITIONAL	0.098
1	18	AR	3951	X-RAY DIFFRACTION	POSITIONAL	0.124
1	19	AS	3951	X-RAY DIFFRACTION	POSITIONAL	0.098
1	20	AT	3951	X-RAY DIFFRACTION	POSITIONAL	0.086
1	21	BA	3951	X-RAY DIFFRACTION	POSITIONAL	0.085
1	22	BB	3951	X-RAY DIFFRACTION	POSITIONAL	0.1
1	23	BC	3951	X-RAY DIFFRACTION	POSITIONAL	0.077
1	24	BD	3951	X-RAY DIFFRACTION	POSITIONAL	0.091
1	25	BE	3951	X-RAY DIFFRACTION	POSITIONAL	0.079
1	26	BF	3951	X-RAY DIFFRACTION	POSITIONAL	0.096
1	27	BG	3951	X-RAY DIFFRACTION	POSITIONAL	0.084
1	28	BH	3951	X-RAY DIFFRACTION	POSITIONAL	0.09
1	29	BI	3951	X-RAY DIFFRACTION	POSITIONAL	0.108
1	30	BJ	3951	X-RAY DIFFRACTION	POSITIONAL	0.11
1	31	BK	3951	X-RAY DIFFRACTION	POSITIONAL	0.099
1	32	BL	3951	X-RAY DIFFRACTION	POSITIONAL	0.291
1	33	BM	3951	X-RAY DIFFRACTION	POSITIONAL	0.107
1	34	BN	3951	X-RAY DIFFRACTION	POSITIONAL	0.095
1	35	BO	3951	X-RAY DIFFRACTION	POSITIONAL	0.095
1	36	BP	3951	X-RAY DIFFRACTION	POSITIONAL	0.252
1	37	BQ	3951	X-RAY DIFFRACTION	POSITIONAL	0.104
1	38	BR	3951	X-RAY DIFFRACTION	POSITIONAL	0.13
1	39	BS	3951	X-RAY DIFFRACTION	POSITIONAL	0.1
1	40	BT	3951	X-RAY DIFFRACTION	POSITIONAL	0.089
1	41	CA	3951	X-RAY DIFFRACTION	POSITIONAL	0.097
1	42	CB	3951	X-RAY DIFFRACTION	POSITIONAL	0.084
1	43	CC	3951	X-RAY DIFFRACTION	POSITIONAL	0.081
1	44	CD	3951	X-RAY DIFFRACTION	POSITIONAL	0.085
1	45	CE	3951	X-RAY DIFFRACTION	POSITIONAL	0.077
1	46	CF	3951	X-RAY DIFFRACTION	POSITIONAL	0.1
1	47	CG	3951	X-RAY DIFFRACTION	POSITIONAL	0.107
1	48	CH	3951	X-RAY DIFFRACTION	POSITIONAL	0.094
1	49	CI	3951	X-RAY DIFFRACTION	POSITIONAL	0.085
1	50	CJ	3951	X-RAY DIFFRACTION	POSITIONAL	0.102
1	51	CK	3951	X-RAY DIFFRACTION	POSITIONAL	0.106
1	52	CL	3951	X-RAY DIFFRACTION	POSITIONAL	0.289
1	53	CM	3951	X-RAY DIFFRACTION	POSITIONAL	0.105
1	54	CN	3951	X-RAY DIFFRACTION	POSITIONAL	0.086
1	55	CO	3951	X-RAY DIFFRACTION	POSITIONAL	0.104
1	56	CP	3951	X-RAY DIFFRACTION	POSITIONAL	0.238
1	57	CQ	3951	X-RAY DIFFRACTION	POSITIONAL	0.099
1	58	CR	3951	X-RAY DIFFRACTION	POSITIONAL	0.172
1	59	CS	3951	X-RAY DIFFRACTION	POSITIONAL	0.09
1	60	CT	3951	X-RAY DIFFRACTION	POSITIONAL	0.079

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 (%)
3-3.0341	0.3525	1409	0.3214	27561	X-RAY DIFFRACTION	63
3.0341-3.0698	0.3314	1836	0.3038	34332	X-RAY DIFFRACTION	79
3.0698-3.1072	0.3066	1817	0.2913	34828	X-RAY DIFFRACTION	80
3.1072-3.1466	0.3077	1835	0.2884	34935	X-RAY DIFFRACTION	80
3.1466-3.188	0.2925	1927	0.2716	35680	X-RAY DIFFRACTION	82
3.188-3.2316	0.2902	1905	0.2736	34942	X-RAY DIFFRACTION	81
3.2316-3.2778	0.2968	1752	0.2676	34579	X-RAY DIFFRACTION	79
3.2778-3.3268	0.278	1961	0.2496	36804	X-RAY DIFFRACTION	84
3.3268-3.3787	0.2566	2048	0.2388	37208	X-RAY DIFFRACTION	86
3.3787-3.4341	0.2543	1998	0.2292	37846	X-RAY DIFFRACTION	87
3.4341-3.4934	0.2533	1980	0.2276	38341	X-RAY DIFFRACTION	88
3.4934-3.5569	0.2405	2092	0.2125	38352	X-RAY DIFFRACTION	89
3.5569-3.6253	0.2337	2057	0.2133	38400	X-RAY DIFFRACTION	88
3.6253-3.6993	0.2261	2119	0.2066	39055	X-RAY DIFFRACTION	90
3.6993-3.7798	0.2065	2013	0.1885	39189	X-RAY DIFFRACTION	90
3.7798-3.8677	0.1978	2080	0.1818	39492	X-RAY DIFFRACTION	91
3.8677-3.9644	0.1954	2113	0.1737	39854	X-RAY DIFFRACTION	92
3.9644-4.0716	0.183	2142	0.1632	39968	X-RAY DIFFRACTION	92
4.0716-4.1914	0.1641	2057	0.1456	40378	X-RAY DIFFRACTION	92
4.1914-4.3267	0.1604	2226	0.1422	40291	X-RAY DIFFRACTION	93
4.3267-4.4814	0.1442	2140	0.1308	40614	X-RAY DIFFRACTION	93
4.4814-4.6608	0.1465	2218	0.133	40788	X-RAY DIFFRACTION	94
4.6608-4.8729	0.1496	2114	0.1342	41075	X-RAY DIFFRACTION	94
4.8729-5.1299	0.15	2176	0.1392	41265	X-RAY DIFFRACTION	95
5.1299-5.4513	0.1742	2116	0.1592	41026	X-RAY DIFFRACTION	94
5.4513-5.8722	0.1865	2162	0.1697	40996	X-RAY DIFFRACTION	94
5.8722-6.4631	0.1794	2142	0.1663	40981	X-RAY DIFFRACTION	94
6.4631-7.3983	0.1643	2110	0.1563	41299	X-RAY DIFFRACTION	95
7.3983-9.3207	0.171	2216	0.1582	41574	X-RAY DIFFRACTION	95
9.3207-135.5646	0.2291	2164	0.2286	41534	X-RAY DIFFRACTION	95

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