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- PDB-5chs: N-terminal domain of the vesicular stomatitis virus L protein -

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Basic information

Entry
Database: PDB / ID: 5chs
TitleN-terminal domain of the vesicular stomatitis virus L protein
ComponentsRNA-directed RNA polymerase L
KeywordsVIRAL PROTEIN / TRANSFERASE / polymerase / virus
Function / homology
Function and homology information


GDP polyribonucleotidyltransferase / virion component => GO:0044423 / negative stranded viral RNA replication / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / Transferases; Transferring one-carbon groups; Methyltransferases / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / host cell cytoplasm / RNA-directed RNA polymerase / RNA-dependent RNA polymerase activity / GTPase activity ...GDP polyribonucleotidyltransferase / virion component => GO:0044423 / negative stranded viral RNA replication / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / Transferases; Transferring one-carbon groups; Methyltransferases / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / host cell cytoplasm / RNA-directed RNA polymerase / RNA-dependent RNA polymerase activity / GTPase activity / ATP binding / metal ion binding
Similarity search - Function
RNA-directed RNA polymerase, rhabdovirus / RNA-directed RNA polymerase L methyltransferase domain, rhabdovirus / Virus-capping methyltransferase, MT domain / Mononegavirales RNA-directed RNA polymerase catalytic domain / Mononegavirus L protein 2-O-ribose methyltransferase / Mononegavirales mRNA-capping domain V / RNA-directed RNA polymerase L, C-terminal / Mononegavirales RNA dependent RNA polymerase / Mononegavirales mRNA-capping region V / RdRp of negative ssRNA viruses with non-segmented genomes catalytic domain profile. / Mononegavirus L protein 2'-O-ribose methyltransferase domain profile.
Similarity search - Domain/homology
RNA-directed RNA polymerase L
Similarity search - Component
Biological speciesVesicular stomatitis Indiana virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / MAD / Resolution: 1.8 Å
AuthorsGreen, T.J. / Qiu, S. / Luo, M.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1R56AI101087 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1R01AI116738 United States
CitationJournal: J.Virol. / Year: 2015
Title: Structure and Function of the N-Terminal Domain of the Vesicular Stomatitis Virus RNA Polymerase.
Authors: Qiu, S. / Ogino, M. / Luo, M. / Ogino, T. / Green, T.J.
History
DepositionJul 10, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 22, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 11, 2015Group: Database references
Revision 1.2Jan 13, 2016Group: Database references
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Refinement description
Category: citation / pdbx_audit_support ...citation / pdbx_audit_support / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization ..._citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation / _software.name
Revision 1.4Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Aug 26, 2020Group: Derived calculations / Structure summary
Category: audit_author / pdbx_struct_conn_angle / struct_conn
Item: _audit_author.name / _pdbx_struct_conn_angle.ptnr1_auth_seq_id ..._audit_author.name / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA-directed RNA polymerase L
B: RNA-directed RNA polymerase L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,9154
Polymers80,6532
Non-polymers2612
Water11,548641
1
A: RNA-directed RNA polymerase L


Theoretical massNumber of molelcules
Total (without water)40,3271
Polymers40,3271
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RNA-directed RNA polymerase L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,5883
Polymers40,3271
Non-polymers2612
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.793, 77.237, 136.533
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein RNA-directed RNA polymerase L / Protein L / Large structural protein / Replicase / Transcriptase


Mass: 40326.629 Da / Num. of mol.: 2 / Fragment: N-terminal domain (UNP residues 36-380)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vesicular stomatitis Indiana virus / Plasmid: pET28b / Production host: Escherichia coli (E. coli)
References: UniProt: Q98776, RNA-directed RNA polymerase, mRNA (guanine-N7)-methyltransferase, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases
#2: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 641 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.12 Å3/Da / Density % sol: 41.92 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 100mM Tris, pH 8.0, 1M NH4Formate, 4% Jeffamine T403 with 0.05% B-octylglucopyranoside

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97932 Å
DetectorType: RAYONIX MX300HS / Detector: CCD / Date: Dec 4, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97932 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 64013 / % possible obs: 99.5 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.03 / Rrim(I) all: 0.073 / Χ2: 1.198 / Net I/av σ(I): 28.2 / Net I/σ(I): 9.9 / Num. measured all: 368628
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.8-1.835.70.41631230.8820.1890.4590.54699.8
1.83-1.865.70.34531830.9130.1560.380.56299.9
1.86-1.95.70.31831530.9270.1450.3510.5899.9
1.9-1.945.80.2631940.9430.1180.2870.605100
1.94-1.985.80.2431800.9590.1090.2650.651100
1.98-2.035.80.20131500.9680.0920.2220.7100
2.03-2.085.80.16931740.9750.0770.1870.738100
2.08-2.135.80.14431830.980.0660.1590.803100
2.13-2.25.80.13132020.9860.0590.1450.872100
2.2-2.275.80.10831950.990.0480.1190.943100
2.27-2.355.80.09931950.9910.0440.1090.992100
2.35-2.445.80.09131910.9910.0410.11.12599.9
2.44-2.555.80.08231900.9930.0360.091.13599.8
2.55-2.695.80.07532150.9950.0330.0821.19899.6
2.69-2.865.80.06532040.9960.0290.0721.33699.5
2.86-3.085.80.06332290.9950.0280.071.78299.3
3.08-3.395.80.05732030.9960.0250.0632.14999.2
3.39-3.885.70.04632350.9970.020.052.23598.8
3.88-4.885.70.04232630.9980.0180.0462.40398.7
4.88-505.40.04533510.9980.020.0492.55696.4

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
SHELXDEphasing
PHENIX1.9_1692refinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
RefinementMethod to determine structure: SIRAS / Resolution: 1.8→37.242 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1998 2000 3.13 %
Rwork0.1735 61945 -
obs0.1744 63945 99.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 108.05 Å2 / Biso mean: 32.0585 Å2 / Biso min: 9.77 Å2
Refinement stepCycle: final / Resolution: 1.8→37.242 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4944 0 17 647 5608
Biso mean--37.95 39.35 -
Num. residues----609
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075065
X-RAY DIFFRACTIONf_angle_d0.9586825
X-RAY DIFFRACTIONf_chiral_restr0.041767
X-RAY DIFFRACTIONf_plane_restr0.004856
X-RAY DIFFRACTIONf_dihedral_angle_d13.3721896
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7983-1.84330.24911370.2114225436296
1.8433-1.89310.21821410.19643754516100
1.8931-1.94880.20071410.183644104551100
1.9488-2.01170.21421430.187244084551100
2.0117-2.08360.22171420.181243894531100
2.0836-2.16710.24921430.17944234566100
2.1671-2.26570.21081420.168744204562100
2.2657-2.38510.24041430.173144314574100
2.3851-2.53450.1881440.178444284572100
2.5345-2.73010.22551430.176944484591100
2.7301-3.00480.19691430.17564434457799
3.0048-3.43930.19041440.1714462460699
3.4393-4.33210.15841450.15664501464699
4.3321-37.24990.19711490.17294591474097
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
10.2918-0.3836-0.17460.92660.07411.40590.0230.04360.2419-0.72820.064-0.0711-1.04420.033-0.21460.5898-0.12830.0970.20770.02990.1937-20.981457.070767.4538
20.8253-1.16680.0911.8279-0.41680.80460.304-0.159-0.806-0.1172-0.0629-0.05840.62530.048-0.07950.4896-0.0534-0.18360.23190.07170.3904-22.839227.472766.7755
32.440.4748-0.35592.168-1.76913.3551-0.05510.1118-0.1179-0.9888-0.0996-0.46150.01170.68520.0970.5697-0.04850.18740.39760.01440.2483-12.652348.823852.0986
40.5640.1992-0.48511.5008-0.372.764-0.0004-0.0877-0.0709-0.0274-0.00720.0009-0.00170.21440.01150.0824-0.0085-0.00120.14590.02490.1312-23.509141.200884.7877
50.73420.5446-0.59552.2511-0.88022.18460.0448-0.0305-0.01080.1094-0.02440.10930.063-0.027-0.02390.07880.0225-0.00750.1537-0.00670.1515-13.8213-2.6838102.1255
61.9986-1.81832.25363.7706-3.08852.99860.03810.80390.475-1.1043-0.3348-0.127-0.071-0.23870.18050.61540.24880.02940.47750.16480.3306-10.554817.441867.6772
70.6511-0.17850.17393.2723-1.62982.00150.29860.15520.3786-0.2415-0.02030.0599-0.3890.0695-0.13040.27880.02380.08650.14390.00960.2079-9.948410.771879.929
80.4960.7742-0.30923.4642-0.31440.9438-0.10340.06910.0428-0.41290.06660.23830.1518-0.03510.03290.1320.0033-0.02650.13890.01190.1495-15.65331.711387.5578
90.969-0.51470.36423.9066-1.06532.9452-0.08970.07130.20270.0093-0.0011-0.1396-0.14620.19790.05480.0619-0.0498-0.0320.19060.03240.2055-6.533125.120697.4321
104.2304-2.51161.5192.1318-1.66022.4634-0.5318-0.09780.57361.22510.33140.0691-0.84760.09160.26950.53320.0136-0.06190.2991-0.00160.3079-9.152437.2935106.7259
113.0452-1.07532.80314.2151-1.58315.5278-0.1451-0.05450.1062-0.0403-0.1363-0.0431-0.26670.43240.23340.0687-0.0136-0.01510.19440.01280.1766-5.336429.360596.1581
123.81523.0562-2.4942.677-1.80921.68290.5359-0.2940.32790.5791-0.38330.6278-0.56770.1498-0.06510.201-0.01030.06810.1981-0.04860.2634-17.349112.802104.946
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 43 through 106 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 107 through 171 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 172 through 204 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 205 through 363 )A0
5X-RAY DIFFRACTION5chain 'B' and (resid 43 through 106 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 107 through 130 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 131 through 171 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 172 through 257 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 258 through 303 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 304 through 328 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 329 through 354 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 355 through 371 )B0

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