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- PDB-8iqd: Crystal structure of AsfvPrimPol N-terminal Prim/Pol domain in co... -

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Basic information

Entry
Database: PDB / ID: 8iqd
TitleCrystal structure of AsfvPrimPol N-terminal Prim/Pol domain in complex with Mn2+ and dCTP
ComponentsPutative primase C962R
KeywordsDNA BINDING PROTEIN / polymerase / primase / PrimPol
Function / homology
Function and homology information


hydrolase activity, acting on acid anhydrides / helicase activity / DNA replication / metal ion binding
Similarity search - Function
Primase, C-terminal 2 / : / Primase C terminal 2 (PriCT-2) / C962R protein N-terminal AEP domain / Domain of unknown function DUF5906 / Family of unknown function (DUF5906) / : / Bacteriophage/plasmid primase, P4, C-terminal / D5 N terminal like / Helicase, superfamily 3, DNA virus ...Primase, C-terminal 2 / : / Primase C terminal 2 (PriCT-2) / C962R protein N-terminal AEP domain / Domain of unknown function DUF5906 / Family of unknown function (DUF5906) / : / Bacteriophage/plasmid primase, P4, C-terminal / D5 N terminal like / Helicase, superfamily 3, DNA virus / Superfamily 3 helicase of DNA viruses domain profile. / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE / : / Putative primase C962R
Similarity search - Component
Biological speciesAfrican swine fever virus BA71V
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.39 Å
AuthorsShao, Z.W. / Gan, J.H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nucleic Acids Res / Year: 2023
Title: Structures and implications of the C962R protein of African swine fever virus.
Authors: Zhiwei Shao / Shichen Su / Jie Yang / Weizhen Zhang / Yanqing Gao / Xin Zhao / Yixi Zhang / Qiyuan Shao / Chulei Cao / Huili Li / Hehua Liu / Jinru Zhang / Jinzhong Lin / Jinbiao Ma / Jianhua Gan /
Abstract: African swine fever virus (ASFV) is highly contagious and can cause lethal disease in pigs. Although it has been extensively studied in the past, no vaccine or other useful treatment against ASFV is ...African swine fever virus (ASFV) is highly contagious and can cause lethal disease in pigs. Although it has been extensively studied in the past, no vaccine or other useful treatment against ASFV is available. The genome of ASFV encodes more than 170 proteins, but the structures and functions for the majority of the proteins remain elusive, which hindered our understanding on the life cycle of ASFV and the development of ASFV-specific inhibitors. Here, we report the structural and biochemical studies of the highly conserved C962R protein of ASFV, showing that C962R is a multidomain protein. The N-terminal AEP domain is responsible for the DNA polymerization activity, whereas the DNA unwinding activity is catalyzed by the central SF3 helicase domain. The middle PriCT2 and D5_N domains and the C-terminal Tail domain all contribute to the DNA unwinding activity of C962R. C962R preferentially works on forked DNA, and likely functions in Base-excision repair (BER) or other repair pathway in ASFV. Although it is not essential for the replication of ASFV, C962R can serve as a model and provide mechanistic insight into the replicative primase proteins from many other species, such as nitratiruptor phage NrS-1, vaccinia virus (VACV) and other viruses.
History
DepositionMar 16, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 26, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative primase C962R
B: Putative primase C962R
C: Putative primase C962R
D: Putative primase C962R
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,94719
Polymers113,4744
Non-polymers2,47315
Water43224
1
A: Putative primase C962R
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0005
Polymers28,3691
Non-polymers6324
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putative primase C962R
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0556
Polymers28,3691
Non-polymers6875
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Putative primase C962R
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9464
Polymers28,3691
Non-polymers5773
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Putative primase C962R
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9464
Polymers28,3691
Non-polymers5773
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)209.160, 42.814, 128.214
Angle α, β, γ (deg.)90.00, 125.04, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Putative primase C962R


Mass: 28368.506 Da / Num. of mol.: 4 / Fragment: N-terminal Prim/Pol domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) African swine fever virus BA71V / Gene: BA71V-C962R, C962R / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0C5B022
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-DCP / 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE


Mass: 467.157 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H16N3O13P3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.07 Å3/Da / Density % sol: 40.61 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1 M SPG buffer pH 8.0 and 25% PEG 1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.97856 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 9, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.39→100.31 Å / Num. obs: 36675 / % possible obs: 97.6 % / Redundancy: 3.2 % / CC1/2: 0.991 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.051 / Rrim(I) all: 0.091 / Χ2: 0.95 / Net I/σ(I): 8.9 / Num. measured all: 115898
Reflection shellResolution: 2.39→2.52 Å / % possible obs: 97.4 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.53 / Num. measured all: 17416 / Num. unique obs: 5290 / CC1/2: 0.827 / Rpim(I) all: 0.343 / Rrim(I) all: 0.633 / Χ2: 0.85 / Net I/σ(I) obs: 2.4

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Processing

Software
NameVersionClassification
PHENIX(1.19.1_4122: ???)refinement
Aimlessdata scaling
XDSdata reduction
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold

Resolution: 2.39→85.62 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 32.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2826 1796 4.91 %
Rwork0.2411 --
obs0.244 36576 96.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.39→85.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6818 0 89 24 6931
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037042
X-RAY DIFFRACTIONf_angle_d0.6019596
X-RAY DIFFRACTIONf_dihedral_angle_d11.4921033
X-RAY DIFFRACTIONf_chiral_restr0.0411099
X-RAY DIFFRACTIONf_plane_restr0.0051233
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.39-2.450.35421710.30992581X-RAY DIFFRACTION96
2.45-2.520.31951430.30172682X-RAY DIFFRACTION98
2.52-2.60.35661400.29832669X-RAY DIFFRACTION98
2.6-2.70.34181360.28642688X-RAY DIFFRACTION98
2.7-2.810.39041390.30442685X-RAY DIFFRACTION99
2.81-2.930.3391530.28492672X-RAY DIFFRACTION98
2.93-3.090.27381270.26622693X-RAY DIFFRACTION98
3.09-3.280.33661290.26812698X-RAY DIFFRACTION98
3.28-3.530.30711140.24272692X-RAY DIFFRACTION97
3.53-3.890.28271530.22732653X-RAY DIFFRACTION96
3.89-4.450.23381150.21012671X-RAY DIFFRACTION96
4.45-5.610.2341230.22062722X-RAY DIFFRACTION96
5.61-85.620.25031530.22392674X-RAY DIFFRACTION92
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)
14.989-0.3614-1.89562.84260.05472.4331-0.043-0.0143-0.061-0.0205-0.05990.20660.04920.03690.0930.3130.0369-0.05470.16090.02490.3492150.171-4.908136.662
24.909-2.0483-1.97234.1831.03852.11530.18190.1120.1158-0.2472-0.1232-0.408-0.04850.0167-0.02220.38370.0468-0.00820.21870.00820.3746187.552-5.309125.997
31.22570.8081-0.3682.94330.87173.40710.2683-0.2609-0.01450.0042-0.348-0.16950.1153-0.63550.0560.3427-0.1079-0.06190.71870.10310.2866185.239-7.719165.819
41.5625-0.2930.54982.5383-1.3765.6446-0.03880.19220.03410.0736-0.1035-0.0554-0.00270.53780.17470.3105-0.0242-0.02330.55540.030.2754153.727-6.74697.086
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 47:272 )A47 - 272
2X-RAY DIFFRACTION2( CHAIN B AND RESID 35:272 )B35 - 272
3X-RAY DIFFRACTION3( CHAIN C AND RESID 20:271 )C20 - 271
4X-RAY DIFFRACTION4( CHAIN D AND RESID 20:271 )D20 - 271

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