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- PDB-6bbo: Crystal structure of human APOBEC3H/RNA complex -

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Basic information

Entry
Database: PDB / ID: 6bbo
TitleCrystal structure of human APOBEC3H/RNA complex
Components
  • APOBEC3H
  • MCherry fluorescent protein
  • RNA (5'-R(*UP*AP*AP*AP*AP*AP*AP*A)-3')
  • RNA (5'-R(*UP*UP*UP*UP*UP*UP*UP*U)-3')
KeywordsHYDROLASE/RNA / APOBEC / deaminase. / HYDROLASE / HYDROLASE-RNA complex
Function / homology
Function and homology information


mRNA Editing: C to U Conversion / Formation of the Editosome / single-stranded DNA cytosine deaminase / DNA cytosine deamination / negative regulation by host of viral genome replication / : / cytidine to uridine editing / cytidine deaminase activity / clearance of foreign intracellular DNA / negative regulation of single stranded viral RNA replication via double stranded DNA intermediate ...mRNA Editing: C to U Conversion / Formation of the Editosome / single-stranded DNA cytosine deaminase / DNA cytosine deamination / negative regulation by host of viral genome replication / : / cytidine to uridine editing / cytidine deaminase activity / clearance of foreign intracellular DNA / negative regulation of single stranded viral RNA replication via double stranded DNA intermediate / : / retrotransposon silencing / bioluminescence / generation of precursor metabolites and energy / P-body / defense response to virus / hydrolase activity / innate immune response / RNA binding / zinc ion binding / nucleoplasm / nucleus / cytosol / 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 / Green fluorescent protein, GFP / Green fluorescent protein-related ...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 / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein
Similarity search - Domain/homology
RNA / APOBEC3H / PAmCherry1 protein / DNA dC->dU-editing enzyme APOBEC-3H / MCherry fluorescent protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Discosoma sp. (sea anemone)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 3.428 Å
AuthorsShaban, N.M. / Shi, K. / Banerjee, S. / Harris, R.S. / Aihara, H.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM118000 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM118047 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA206309 United States
CitationJournal: Mol. Cell / Year: 2018
Title: The Antiviral and Cancer Genomic DNA Deaminase APOBEC3H Is Regulated by an RNA-Mediated Dimerization Mechanism.
Authors: Shaban, N.M. / Shi, K. / Lauer, K.V. / Carpenter, M.A. / Richards, C.M. / Salamango, D. / Wang, J. / Lopresti, M.W. / Banerjee, S. / Levin-Klein, R. / Brown, W.L. / Aihara, H. / Harris, R.S.
History
DepositionOct 19, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 10, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 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 / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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 / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: APOBEC3H
B: RNA (5'-R(*UP*AP*AP*AP*AP*AP*AP*A)-3')
C: RNA (5'-R(*UP*UP*UP*UP*UP*UP*UP*U)-3')
D: MCherry fluorescent protein
E: APOBEC3H
F: RNA (5'-R(*UP*AP*AP*AP*AP*AP*AP*A)-3')
G: RNA (5'-R(*UP*UP*UP*UP*UP*UP*UP*U)-3')
H: MCherry fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,86112
Polymers102,5468
Non-polymers3154
Water00
1
A: APOBEC3H
B: RNA (5'-R(*UP*AP*AP*AP*AP*AP*AP*A)-3')
C: RNA (5'-R(*UP*UP*UP*UP*UP*UP*UP*U)-3')
D: MCherry fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,4306
Polymers51,2734
Non-polymers1582
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: APOBEC3H
F: RNA (5'-R(*UP*AP*AP*AP*AP*AP*AP*A)-3')
G: RNA (5'-R(*UP*UP*UP*UP*UP*UP*UP*U)-3')
H: MCherry fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,4306
Polymers51,2734
Non-polymers1582
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)101.293, 101.293, 211.217
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number151
Space group name H-MP3112
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: -y,-x,-z+2/3
#5: -x+y,y,-z+1/3
#6: x,x-y,-z
Components on special symmetry positions
IDModelComponents
11B-4-

A

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Components

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Protein , 2 types, 4 molecules AEDH

#1: Protein APOBEC3H


Mass: 21415.682 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: APOBEC3H / Production host: Escherichia coli (E. coli) / References: UniProt: B7TQM6, UniProt: Q6NTF7*PLUS
#4: Protein MCherry fluorescent protein


Mass: 24887.143 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Discosoma sp. (sea anemone) / Production host: Escherichia coli (E. coli) / References: UniProt: X5DSL3, UniProt: D1MPT3*PLUS

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RNA chain , 2 types, 4 molecules BFCG

#2: RNA chain RNA (5'-R(*UP*AP*AP*AP*AP*AP*AP*A)-3')


Mass: 2565.649 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#3: RNA chain RNA (5'-R(*UP*UP*UP*UP*UP*UP*UP*U)-3')


Mass: 2404.369 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)

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Non-polymers , 2 types, 4 molecules

#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3

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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: 3.14 Å3/Da / Density % sol: 60.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: NaI, PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Aug 23, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.42822287772→49.2504239036 Å / Num. obs: 16797 / % possible obs: 99.9 % / Redundancy: 4.7 % / Biso Wilson estimate: 110.026451622 Å2 / Rmerge(I) obs: 0.188 / Rrim(I) all: 0.241 / Net I/σ(I): 5.5
Reflection shellResolution: 3.45→3.78 Å / Redundancy: 4.6 % / Rmerge(I) obs: 1.554 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 3988 / CC1/2: 0.494 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIXdev_2926refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 6b0b

6b0b


Resolution: 3.428→49.25 Å / SU ML: 0.7 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 46.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3921 866 5.3 %
Rwork0.3637 --
obs0.3652 16346 96.35 %
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.428→49.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6264 656 14 0 6934
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0027160
X-RAY DIFFRACTIONf_angle_d0.5659784
X-RAY DIFFRACTIONf_dihedral_angle_d14.0764224
X-RAY DIFFRACTIONf_chiral_restr0.0391050
X-RAY DIFFRACTIONf_plane_restr0.0031144
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4282-3.64290.44721080.43422163X-RAY DIFFRACTION81
3.6429-3.92410.46451600.4052614X-RAY DIFFRACTION99
3.9241-4.31880.42891310.37972646X-RAY DIFFRACTION99
4.3188-4.94320.39531590.36332640X-RAY DIFFRACTION99
4.9432-6.2260.37751590.39612670X-RAY DIFFRACTION100
6.226-49.25550.35671490.32292747X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 11.8962 Å / Origin y: 20.6338 Å / Origin z: 17.5858 Å
111213212223313233
T0.0387 Å20.0978 Å2-0.2447 Å2--0.2701 Å20.2371 Å2---0.3469 Å2
L1.891 °20.2607 °2-0.4439 °2-1.8233 °20.275 °2--2.0731 °2
S0.2536 Å °-0.1781 Å °0.3506 Å °-0.0431 Å °0.3727 Å °-0.3572 Å °-0.2073 Å °0.4559 Å °0.64 Å °
Refinement TLS groupSelection details: all

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