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- PDB-8cz5: N11 P domain 2D9 Fab P complex -

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Basic information

Entry
Database: PDB / ID: 8cz5
TitleN11 P domain 2D9 Fab P complex
Components
  • Fab 2D9 Heavy Chain
  • Fab 2D9 Light Chain
  • N11 P domain
KeywordsVIRAL PROTEIN/Immune System / RHDV-Fab / VIRAL PROTEIN / VIRAL PROTEIN-Immune System complex
Function / homology
Function and homology information


RNA-protein covalent cross-linking / ribonucleoside triphosphate phosphatase activity / viral capsid / host cell cytoplasm / RNA helicase activity / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / proteolysis ...RNA-protein covalent cross-linking / ribonucleoside triphosphate phosphatase activity / viral capsid / host cell cytoplasm / RNA helicase activity / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / proteolysis / RNA binding / ATP binding / cytoplasm
Similarity search - Function
Caliciviridae (CV) 3C-like protein profile. / Peptidase C24, Calicivirus polyprotein Orf1 / 2C endopeptidase (C24) cysteine protease family / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / Calicivirus coat protein / Calicivirus coat protein / 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 ...Caliciviridae (CV) 3C-like protein profile. / Peptidase C24, Calicivirus polyprotein Orf1 / 2C endopeptidase (C24) cysteine protease family / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / Calicivirus coat protein / Calicivirus coat protein / 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 / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ACETATE ION / : / Genome polyprotein
Similarity search - Component
Biological speciesLagovirus
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.645 Å
AuthorsLeuthold, M. / Kilic, T. / Hansman, G.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
CitationJournal: J.Virol. / Year: 2022
Title: Structural Basis for Rabbit Hemorrhagic Disease Virus Antibody Specificity.
Authors: Leuthold, M.M. / Kilic, T. / Devant, J.M. / Landeta, O. / Parra, F. / Dalton, K.P. / Hansman, G.S.
History
DepositionMay 24, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 19, 2022Provider: repository / Type: Initial release
Revision 1.1May 3, 2023Group: Database references / Category: 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
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: N11 P domain
H: Fab 2D9 Heavy Chain
L: Fab 2D9 Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,3848
Polymers81,9823
Non-polymers4025
Water73941
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)92.290, 92.290, 493.070
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

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Protein , 1 types, 1 molecules A

#1: Protein N11 P domain / p254


Mass: 34342.941 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lagovirus / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0B5CYZ3

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Antibody , 2 types, 2 molecules HL

#2: Antibody Fab 2D9 Heavy Chain


Mass: 24128.086 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#3: Antibody Fab 2D9 Light Chain


Mass: 23510.900 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)

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Non-polymers , 3 types, 46 molecules

#4: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cd / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 41 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.67 Å3/Da / Density % sol: 66.48 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / Details: 0.1 M citric acid (pH 4) and 30 % PEG 6000

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Data collection

DiffractionMean temperature: 291.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 26, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.645→48.807 Å / Num. obs: 37731 / % possible obs: 99.68 % / Redundancy: 6 % / Biso Wilson estimate: 54.54 Å2 / CC1/2: 0.763 / Net I/σ(I): 1.37
Reflection shellResolution: 2.645→48.807 Å / Mean I/σ(I) obs: 10.79 / Num. unique obs: 37731 / CC1/2: 0.763 / % possible all: 99.88

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Processing

Software
NameVersionClassification
PHENIX1.13refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4X1W

4x1w


Resolution: 2.645→48.807 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 22.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2234 1887 5 %
Rwork0.1938 --
obs0.1953 37731 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.645→48.807 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5624 0 14 41 5679
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035804
X-RAY DIFFRACTIONf_angle_d0.6097970
X-RAY DIFFRACTIONf_dihedral_angle_d2.7913650
X-RAY DIFFRACTIONf_chiral_restr0.044901
X-RAY DIFFRACTIONf_plane_restr0.0041038
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6451-2.71660.38461390.31092651X-RAY DIFFRACTION98
2.7166-2.79650.29221410.28122672X-RAY DIFFRACTION100
2.7965-2.88680.29581420.26012691X-RAY DIFFRACTION100
2.8868-2.98990.2841420.24762695X-RAY DIFFRACTION100
2.9899-3.10960.24571420.23592700X-RAY DIFFRACTION100
3.1096-3.25110.27091420.232708X-RAY DIFFRACTION100
3.2511-3.42250.27041440.21762734X-RAY DIFFRACTION100
3.4225-3.63690.25571440.20162725X-RAY DIFFRACTION100
3.6369-3.91760.20791440.18712752X-RAY DIFFRACTION100
3.9176-4.31160.17941460.15512770X-RAY DIFFRACTION100
4.3116-4.9350.16311470.13342781X-RAY DIFFRACTION99
4.935-6.21550.15851510.16232868X-RAY DIFFRACTION100
6.2155-48.8070.2441630.20193097X-RAY DIFFRACTION100
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)
13.37160.2417-1.41862.51641.62022.85240.47431.18270.7727-0.2043-0.30050.3079-0.12020.47150.00030.49640.08720.04460.5224-0.03590.533814.4921-18.0536-16.4103
22.5406-1.65840.33344.58510.59371.518-0.1319-0.1464-0.1979-0.09930.11120.06630.0997-0.0131-0.09030.4315-0.0030.03090.5074-0.08260.4274-2.473-8.7636-13.5694
30.635-0.3191-0.54172.27231.0140.78090.28920.11580.0552-0.4704-0.2080.23940.1996-0.35690.01760.54630.01040.02030.6174-0.09380.5817-9.38240.3916-12.8585
40.5268-0.2625-0.02670.23770.22830.13830.55620.04581.0182-0.9219-0.2382-0.4727-0.447-0.488-0.00240.60690.1373-0.03760.6739-0.05060.7843-2.2226-1.9467-22.8092
51.24130.06471.15612.44160.98391.2485-0.0632-0.6327-0.22610.25630.2395-0.1829-0.2186-0.0855-0.08280.5724-0.0258-0.0540.4621-0.07120.363256.1596-42.538341.5533
61.252-0.60040.26691.6761-0.20321.41030.06490.1998-0.1572-0.0549-0.08380.11670.1867-0.06220.03970.4472-0.0259-0.03870.3624-0.08940.362141.6791-33.726830.1416
71.17690.08360.25951.760.61670.393-0.0490.3710.2284-0.23040.0052-0.4783-0.62440.17160.0660.52890.0295-0.02510.41530.01250.470945.5584-31.027224.1578
80.62850.27150.61820.9270.01331.6215-0.02440.0291-0.0081-0.0183-0.09620.1479-0.0102-0.12680.0670.4008-0.0104-0.02890.382-0.05970.376533.1752-27.483831.9665
92.5747-1.3757-0.10382.0632-0.00380.8542-0.0433-0.0637-0.21210.12190.0269-0.02390.22390.1939-0.02330.49830.0341-0.05270.3318-0.08620.360849.4189-47.62737.8955
102.0849-0.05910.12821.1312-0.3380.62170.0483-0.0511-0.09420.37020.0849-0.28120.38280.3631-0.01340.6770.1423-0.06740.5655-0.07280.450154.5633-57.575343.2118
111.9625-1.3789-0.14611.4362-0.28070.07660.11740.1581-0.15950.1246-0.08590.18910.0312-0.0039-0.05330.4572-0.013-0.03960.4609-0.14830.501311.4245-27.995818.9924
120.4758-0.48780.86250.1143-0.4951.39290.1367-0.0654-0.2113-0.07970.0180.05620.1427-0.0979-0.13420.3846-0.1126-0.02590.382-0.08610.44296.9659-24.518511.7338
130.14420.0673-0.72481.8541-0.56282.9809-0.04080.1881-0.3085-0.841-0.57140.4761-0.4856-0.37750.27030.68810.0004-0.10140.6666-0.18890.6948-11.2368-13.5999-18.4248
140.37250.1462-0.24371.44511.14253.8622-0.29890.05480.05780.0103-0.07350.36510.8196-0.6330.18470.6345-0.07980.02050.5652-0.12160.5001-9.9318-20.6449-10.7092
154.09512.467-1.93514.53530.02531.38910.3784-0.04240.2914-0.16040.02910.53151.1179-0.9230.08910.6081-0.2865-0.09750.6873-0.14450.6335-19.6084-18.8982-13.1708
161.12790.321.28851.37380.76372.8074-0.13660.5279-0.2016-0.1606-0.0382-0.1338-0.4220.35860.02950.36930.0047-0.02740.4282-0.04890.37127.0074-19.31171.3716
172.2231-0.8657-1.86662.471-0.66242.68570.21520.2799-0.5133-0.3723-0.1271-0.01640.74720.30290.09180.51240.0369-0.07660.6099-0.09850.363927.7079-28.64720.5209
181.23130.26111.021.09340.35172.9235-0.12870.26630.42310.1201-0.3043-0.08350.37390.0898-0.06660.30260.0105-0.04430.47560.01030.396823.3874-23.41193.3468
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'L' and (resid 102 through 113 )
2X-RAY DIFFRACTION2chain 'L' and (resid 114 through 174 )
3X-RAY DIFFRACTION3chain 'L' and (resid 175 through 197 )
4X-RAY DIFFRACTION4chain 'L' and (resid 198 through 213 )
5X-RAY DIFFRACTION5chain 'A' and (resid 237 through 260 )
6X-RAY DIFFRACTION6chain 'A' and (resid 261 through 319 )
7X-RAY DIFFRACTION7chain 'A' and (resid 320 through 339 )
8X-RAY DIFFRACTION8chain 'A' and (resid 340 through 431 )
9X-RAY DIFFRACTION9chain 'A' and (resid 432 through 536 )
10X-RAY DIFFRACTION10chain 'A' and (resid 537 through 569 )
11X-RAY DIFFRACTION11chain 'H' and (resid 1 through 76 )
12X-RAY DIFFRACTION12chain 'H' and (resid 77 through 133 )
13X-RAY DIFFRACTION13chain 'H' and (resid 134 through 154 )
14X-RAY DIFFRACTION14chain 'H' and (resid 155 through 211 )
15X-RAY DIFFRACTION15chain 'H' and (resid 212 through 222 )
16X-RAY DIFFRACTION16chain 'L' and (resid 1 through 38 )
17X-RAY DIFFRACTION17chain 'L' and (resid 39 through 75 )
18X-RAY DIFFRACTION18chain 'L' and (resid 76 through 101 )

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