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- PDB-2b43: Crystal structure of the Norwalk virus RNA dependent RNA polymera... -

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Basic information

Entry
Database: PDB / ID: 2b43
TitleCrystal structure of the Norwalk virus RNA dependent RNA polymerase from strain Hu/NLV/Dresden174/1997/GE
Componentsnon-structural polyprotein
KeywordsVIRAL PROTEIN / RNA / polymerase
Function / homology
Function and homology information


calicivirin / RNA-protein covalent cross-linking / ribonucleoside triphosphate phosphatase activity / nucleoside-triphosphate phosphatase / RNA helicase activity / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription ...calicivirin / RNA-protein covalent cross-linking / ribonucleoside triphosphate phosphatase activity / nucleoside-triphosphate phosphatase / RNA helicase activity / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / RNA binding / ATP binding
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #3230 / Viral polyprotein, Caliciviridae N-terminal / Viral polyprotein N-terminal / Norovirus 3C-like protease (NV 3CLpro) domain profile. / Norovirus peptidase C37 / Southampton virus-type processing peptidase / Mitochondrial Import Receptor Subunit Tom20; Chain A - #20 / Mitochondrial Import Receptor Subunit Tom20; Chain A / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Reverse transcriptase/Diguanylate cyclase domain ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #3230 / Viral polyprotein, Caliciviridae N-terminal / Viral polyprotein N-terminal / Norovirus 3C-like protease (NV 3CLpro) domain profile. / Norovirus peptidase C37 / Southampton virus-type processing peptidase / Mitochondrial Import Receptor Subunit Tom20; Chain A - #20 / Mitochondrial Import Receptor Subunit Tom20; Chain A / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Reverse transcriptase/Diguanylate cyclase domain / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase / Helix non-globular / Special / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Reverse transcriptase/Diguanylate cyclase domain / Alpha-Beta Plaits / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesNorovirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsHogbom, M. / Rohayem, J. / Unge, T. / Jones, T.A.
CitationJournal: To be Published
Title: Crystal structure of the Norwalk virus RNA dependent RNA polymerase from strain Hu/NLV/Dresden174/1997/GE
Authors: Hogbom, M. / Rohayem, J. / Unge, T. / Jones, T.A.
History
DepositionSep 22, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 4, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: non-structural polyprotein
B: non-structural polyprotein
C: non-structural polyprotein
D: non-structural polyprotein


Theoretical massNumber of molelcules
Total (without water)234,6314
Polymers234,6314
Non-polymers00
Water20,2131122
1
A: non-structural polyprotein


Theoretical massNumber of molelcules
Total (without water)58,6581
Polymers58,6581
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: non-structural polyprotein


Theoretical massNumber of molelcules
Total (without water)58,6581
Polymers58,6581
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: non-structural polyprotein


Theoretical massNumber of molelcules
Total (without water)58,6581
Polymers58,6581
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: non-structural polyprotein


Theoretical massNumber of molelcules
Total (without water)58,6581
Polymers58,6581
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.470, 125.560, 218.130
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: 4 / Auth seq-ID: 6 - 506 / Label seq-ID: 7 - 507

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD

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Components

#1: Protein
non-structural polyprotein


Mass: 58657.762 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Norovirus / Genus: Norovirus / Production host: Escherichia coli (E. coli) / References: UniProt: Q6REV3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1122 / 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: 2.6 Å3/Da / Density % sol: 53 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Sodium Citrate, Sodium Cacodylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.94995 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 17, 2005
RadiationMonochromator: Silicon (1 1 1) channel-cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.94995 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. all: 107725 / Num. obs: 107725 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Rsym value: 0.085 / Net I/σ(I): 12.7
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 3.11 / Num. unique all: 12568 / Rsym value: 0.374 / % possible all: 95.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→20 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.913 / SU B: 13.772 / SU ML: 0.178 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.316 / ESU R Free: 0.246 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25654 5372 5 %RANDOM
Rwork0.19232 ---
all0.19554 102225 --
obs0.19554 102225 97.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.932 Å2
Baniso -1Baniso -2Baniso -3
1-1.19 Å20 Å20 Å2
2--0.44 Å20 Å2
3----1.63 Å2
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15716 0 0 1122 16838
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02216124
X-RAY DIFFRACTIONr_angle_refined_deg1.4331.97321868
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.53152000
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.71323.929672
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.227152796
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2621596
X-RAY DIFFRACTIONr_chiral_restr0.1020.22368
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212184
X-RAY DIFFRACTIONr_nbd_refined0.2180.27851
X-RAY DIFFRACTIONr_nbtor_refined0.3050.210916
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.21201
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1760.265
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1580.228
X-RAY DIFFRACTIONr_mcbond_it0.6761.510244
X-RAY DIFFRACTIONr_mcangle_it1.106216220
X-RAY DIFFRACTIONr_scbond_it1.61636685
X-RAY DIFFRACTIONr_scangle_it2.6244.55648
Refine LS restraints NCS

Ens-ID: 1 / Number: 3929 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Amedium positional0.40.5
2Bmedium positional0.40.5
3Cmedium positional0.440.5
4Dmedium positional0.330.5
1Amedium thermal0.552
2Bmedium thermal0.572
3Cmedium thermal0.612
4Dmedium thermal0.572
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 387 -
Rwork0.23 7251 -
obs--95.25 %
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)
10.69510.11410.14120.57880.18231.26740.0074-0.081-0.03010.03930.05580.03280.09610.0148-0.0632-0.0795-0.01510.0042-0.056-0.0326-0.0403-3.04323.205-0.971
20.7125-0.24620.44290.635-0.28851.61330.01190.12880.03850.00020.0599-0.05540.0452-0.0246-0.0718-0.06440.0051-0.0269-0.03290.0411-0.02-39.71222.097-54.685
30.56610.041-0.07840.6590.13011.1598-0.0051-0.0865-0.02630.02370.0632-0.02750.09170.0432-0.0581-0.07020.0029-0.0083-0.06490.0125-0.0709-38.079-22.146-1.047
40.9928-0.26750.05990.8467-0.12531.23720.04370.27330.0825-0.0255-0.0351-0.02880.05590.1219-0.0087-0.1060.00890.00310.05690.0125-0.0681-5.106-23.576-52.706
52.51550.8022.06091.08930.71144.07240.1683-0.0814-0.39690.31830.0514-0.19290.3283-0.0177-0.21980.07380.0392-0.0697-0.1157-0.01290.0006-6.293-4.874-6.24
62.767-0.39412.57421.28970.07673.73280.20280.247-0.2428-0.3507-0.01840.12650.22390.1197-0.18450.0997-0.0125-0.0746-0.04980.0043-0.0682-36.969-5.727-48.295
71.37910.0063-2.0351.10920.50843.31240.04890.02620.1329-0.01620.02660.0488-0.02390.1242-0.0756-0.09560.0225-0.0407-0.0824-0.0029-0.0698-36.5296.704-6.354
82.7262-1.1408-2.44240.75880.63222.75520.44270.45070.5614-0.2085-0.2204-0.2747-0.3528-0.1292-0.22230.08780.0190.07440.11950.11660.0601-6.6995.405-48.908
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA6 - 247 - 25
2X-RAY DIFFRACTION1AA42 - 40343 - 404
3X-RAY DIFFRACTION2BB6 - 247 - 25
4X-RAY DIFFRACTION2BB42 - 40343 - 404
5X-RAY DIFFRACTION3CC6 - 247 - 25
6X-RAY DIFFRACTION3CC42 - 40343 - 404
7X-RAY DIFFRACTION4DD6 - 247 - 25
8X-RAY DIFFRACTION4DD42 - 40343 - 404
9X-RAY DIFFRACTION5AA25 - 4126 - 42
10X-RAY DIFFRACTION5AA404 - 506405 - 507
11X-RAY DIFFRACTION6BB25 - 4126 - 42
12X-RAY DIFFRACTION6BB404 - 506405 - 507
13X-RAY DIFFRACTION7CC25 - 4126 - 42
14X-RAY DIFFRACTION7CC404 - 506405 - 507
15X-RAY DIFFRACTION8DD25 - 4126 - 42
16X-RAY DIFFRACTION8DD404 - 506405 - 507

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