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- PDB-5z98: Crystal Structure of the Primate APOBEC3H Dimer mediated by RNA Duplex -

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Basic information

Entry
Database: PDB / ID: 5z98
TitleCrystal Structure of the Primate APOBEC3H Dimer mediated by RNA Duplex
Components
  • Apolipoprotein B mRNA editing enzyme catalytic polypeptide-like protein 3H
  • RNA (5'-R(*AP*UP*AP*CP*CP*CP*GP*GP*CP*A)-3')
  • RNA (5'-R(P*CP*UP*GP*CP*CP*GP*GP*GP*UP*A)-3')
KeywordsANTIVIRAL PROTEIN/RNA / APOBEC3 / APOBEC3H / cytidine deaminase / deaminase / anti-HIV / Vif / dsRNA / cancer / HIV-1 / SIV / chimpanzee / dimerization / Pan troglodytes / ANTIVIRAL PROTEIN-RNA complex
Function / homology
Function and homology information


single-stranded DNA cytosine deaminase / hydrolase activity / zinc ion binding / cytoplasm
Similarity search - Function
APOBEC3H / APOBEC3 / : / APOBEC/CMP deaminase, zinc-binding / Cytidine and deoxycytidylate deaminases zinc-binding region signature. / Cytidine and deoxycytidylate deaminase domain / Cytidine and deoxycytidylate deaminases domain profile. / Cytidine deaminase-like
Similarity search - Domain/homology
RNA / single-stranded DNA cytosine deaminase
Similarity search - Component
Biological speciesPan troglodytes (chimpanzee)
unidentified (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsMatsuoka, T. / Nagae, T. / Ode, H. / Watanabe, N. / Iwatani, Y.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of ScienceJP15H04740 Japan
CitationJournal: Nucleic Acids Res. / Year: 2018
Title: Structural basis of chimpanzee APOBEC3H dimerization stabilized by double-stranded RNA.
Authors: Matsuoka, T. / Nagae, T. / Ode, H. / Awazu, H. / Kurosawa, T. / Hamano, A. / Matsuoka, K. / Hachiya, A. / Imahashi, M. / Yokomaku, Y. / Watanabe, N. / Iwatani, Y.
History
DepositionFeb 2, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 15, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 14, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Apolipoprotein B mRNA editing enzyme catalytic polypeptide-like protein 3H
B: Apolipoprotein B mRNA editing enzyme catalytic polypeptide-like protein 3H
C: RNA (5'-R(P*CP*UP*GP*CP*CP*GP*GP*GP*UP*A)-3')
D: RNA (5'-R(*AP*UP*AP*CP*CP*CP*GP*GP*CP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,3086
Polymers50,1784
Non-polymers1312
Water1,38777
1
B: Apolipoprotein B mRNA editing enzyme catalytic polypeptide-like protein 3H
C: RNA (5'-R(P*CP*UP*GP*CP*CP*GP*GP*GP*UP*A)-3')
D: RNA (5'-R(*AP*UP*AP*CP*CP*CP*GP*GP*CP*A)-3')
hetero molecules

A: Apolipoprotein B mRNA editing enzyme catalytic polypeptide-like protein 3H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,3086
Polymers50,1784
Non-polymers1312
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_556x,y,z+11
Buried area4520 Å2
ΔGint-111 kcal/mol
Surface area21020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.341, 86.970, 77.363
Angle α, β, γ (deg.)90.00, 102.63, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Apolipoprotein B mRNA editing enzyme catalytic polypeptide-like protein 3H / DNA dC->dU-editing enzyme APOBEC-3H


Mass: 21912.309 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pan troglodytes (chimpanzee) / Gene: APOBEC3H / Production host: Escherichia coli (E. coli) / References: UniProt: B7T0U6
#2: RNA chain RNA (5'-R(P*CP*UP*GP*CP*CP*GP*GP*GP*UP*A)-3')


Mass: 3192.948 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) unidentified (others) / Production host: Escherichia coli (E. coli)
#3: RNA chain RNA (5'-R(*AP*UP*AP*CP*CP*CP*GP*GP*CP*A)-3')


Mass: 3159.965 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) unidentified (others) / Production host: Escherichia coli (E. coli)
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.54 Å3/Da / Density % sol: 51.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 10% PEG 3350, 100mM ammonium formate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 7, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→43.49 Å / Num. obs: 24557 / % possible obs: 97.3 % / Redundancy: 3.1 % / CC1/2: 0.996 / Rmerge(I) obs: 0.073 / Net I/σ(I): 8.5
Reflection shellResolution: 2.2→2.27 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.471 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 2074 / CC1/2: 0.876 / % possible all: 94.7

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5w3v

5w3v


Resolution: 2.2→43.485 Å / SU ML: 0.34 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 42.36
RfactorNum. reflection% reflection
Rfree0.3202 1188 4.86 %
Rwork0.2511 --
obs0.2545 24454 96.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.2→43.485 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3028 370 2 77 3477
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083516
X-RAY DIFFRACTIONf_angle_d1.014830
X-RAY DIFFRACTIONf_dihedral_angle_d9.7352097
X-RAY DIFFRACTIONf_chiral_restr0.047522
X-RAY DIFFRACTIONf_plane_restr0.006558
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.30020.42811360.35612844X-RAY DIFFRACTION95
2.3002-2.42140.37851330.35192879X-RAY DIFFRACTION96
2.4214-2.57310.40581650.32822931X-RAY DIFFRACTION98
2.5731-2.77180.3911590.32941X-RAY DIFFRACTION98
2.7718-3.05060.34721580.2832897X-RAY DIFFRACTION98
3.0506-3.49190.32811350.25432937X-RAY DIFFRACTION97
3.4919-4.39880.32741340.21712895X-RAY DIFFRACTION96
4.3988-43.49350.24861680.20442942X-RAY DIFFRACTION97

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