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- PDB-6b0b: Crystal structure of human APOBEC3H -

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Basic information

Entry
Database: PDB / ID: 6b0b
TitleCrystal structure of human APOBEC3H
Components
  • APOBEC3H
  • MCherry
  • 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


regulation of macromolecule biosynthetic process / mRNA Editing: C to U Conversion / Formation of the Editosome / single-stranded DNA cytosine deaminase / negative regulation of single stranded viral RNA replication via double stranded DNA intermediate / DNA cytosine deamination / cytidine to uridine editing / negative regulation by host of viral genome replication / clearance of foreign intracellular DNA / cytidine deaminase activity ...regulation of macromolecule biosynthetic process / mRNA Editing: C to U Conversion / Formation of the Editosome / single-stranded DNA cytosine deaminase / negative regulation of single stranded viral RNA replication via double stranded DNA intermediate / DNA cytosine deamination / cytidine to uridine editing / negative regulation by host of viral genome replication / clearance of foreign intracellular DNA / cytidine deaminase activity / transposable element 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 / single-stranded DNA cytosine deaminase / PAmCherry1 protein / DNA dC->dU-editing enzyme APOBEC-3H / :
Similarity search - Component
Biological speciesHomo sapiens (human)
Discosoma sp. (sea anemone)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.28006215294 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
DepositionSep 14, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 25, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Database references / Category: citation_author
Revision 1.2Jan 10, 2018Group: Database references / Structure summary / Category: audit_author / citation / citation_author
Item: _audit_author.name / _citation.journal_abbrev ..._audit_author.name / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.3Jan 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 1.4Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_conn_type / struct_ncs_dom_lim
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 / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_alt_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_alt_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_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
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,30110
Polymers112,1708
Non-polymers1312
Water362
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,1505
Polymers56,0854
Non-polymers651
Water181
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,1505
Polymers56,0854
Non-polymers651
Water181
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.)90.000, 90.000, 120.000
Int Tables number151
Space group name H-MP3112
Space group name HallP312(x,y,z+1/3)
Components on special symmetry positions
IDModelComponents
11B-4-

A

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22
13
23
14
24

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-IDBeg label alt-IDEnd label alt-ID
111LEULEULEULEUchain 'A'AA3 - 346 - 37
121PROPROGLNGLNchain 'A'AA36 - 18239 - 185
211LEULEULEULEUchain 'E'EE3 - 346 - 37
221PROPROGLNGLNchain 'E'EE36 - 18239 - 185
112UUUUchain 'C'CC0 - 71 - 8
212UUUUchain 'G'GG0 - 71 - 8
113UUAAchain 'B'BB0 - 71 - 8
213UUAAchain 'F'FF0 - 71 - 8
114ASNASNGLYGLYchain 'D'DD4 - 5132 - 79AA
124LEULEUPHEPHEchain 'D'DD54 - 6582 - 93AA
134LYSLYSSERSERchain 'D'DD70 - 11298 - 140AA
144PHEPHETYRTYRchain 'D'DD118 - 151146 - 179AA
154ALAALASERSERchain 'D'DD156 - 222184 - 250AA
214ASNASNGLYGLYchain 'H'HH4 - 5132 - 79AA
224LEULEUPHEPHEchain 'H'HH54 - 6582 - 93AA
234LYSLYSSERSERchain 'H'HH70 - 11298 - 140AA
244PHEPHETYRTYRchain 'H'HH118 - 151146 - 179AA
254ALAALASERSERchain 'H'HH156 - 222184 - 250AA

NCS ensembles :
ID
1
2
3
4

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Components

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Protein , 2 types, 4 molecules AEDH

#1: Protein APOBEC3H


Mass: 21976.305 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


Mass: 28832.373 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: V9VHH0, 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: 2710.535 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.14 Å3/Da / Density % sol: 60.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: NH4I, PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.28 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: 1.28 Å / Relative weight: 1
ReflectionResolution: 3.28→49.3 Å / Num. obs: 366518 / % possible obs: 98.3 % / Redundancy: 20.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.21 / Rpim(I) all: 0.048 / Rsym value: 0.21 / Net I/σ(I): 13.4
Reflection shellResolution: 3.28→3.48 Å / Redundancy: 21.1 % / Rmerge(I) obs: 3.2 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 37356 / CC1/2: 0.5 / Rsym value: 3.2 / % possible all: 89

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Processing

Software
NameVersionClassification
PHENIXdev_2926refinement
XDSdata reduction
XDSdata scaling
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 3.28006215294→49.2504239036 Å / SU ML: 0.767480575866 / Cross valid method: FREE R-VALUE / σ(F): 1.32615988547 / Phase error: 52.6380330778 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.362444912965 967 5.12399321747 %
Rwork0.352660864449 17905 -
obs0.353353535773 18872 97.5397973951 %
Solvent computationShrinkage radii: 1.1 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 203.283025169 Å2
Refinement stepCycle: LAST / Resolution: 3.28006215294→49.2504239036 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6272 656 2 2 6932
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.001850803970357158
X-RAY DIFFRACTIONf_angle_d0.573993500839784
X-RAY DIFFRACTIONf_chiral_restr0.03902243103571050
X-RAY DIFFRACTIONf_plane_restr0.003056121540031146
X-RAY DIFFRACTIONf_dihedral_angle_d14.33437691184226
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2801-3.4530.5209777193391340.5273192676032256X-RAY DIFFRACTION87.2262773723
3.453-3.66920.5644289850361250.4483115957112555X-RAY DIFFRACTION97.7388767323
3.6692-3.95240.4160989943571330.4233191392252578X-RAY DIFFRACTION99.6324880559
3.9524-4.34990.4027139021911320.3672458490682608X-RAY DIFFRACTION99.3473531545
4.3499-4.97890.3588104365551140.3566959244012612X-RAY DIFFRACTION99.416484318
4.9789-6.27080.4096977394461470.3991688872562634X-RAY DIFFRACTION99.7131588383
6.2708-49.2560.3085768745441820.2938565571692662X-RAY DIFFRACTION99.5798319328
Refinement TLS params.Method: refined / Origin x: 11.9001237501 Å / Origin y: 20.6400823672 Å / Origin z: 17.5855038836 Å
111213212223313233
T-0.0855085226805 Å20.0882467353178 Å2-0.10790807101 Å2--0.319847027373 Å20.0120392477742 Å2---0.600106884924 Å2
L2.85193416596 °20.886203248454 °2-1.67302049605 °2-3.7503729156 °20.618611348723 °2--2.86203856806 °2
S-0.0587789354703 Å °0.437003517793 Å °0.678858803063 Å °0.24476481393 Å °0.451033217994 Å °-0.401262496598 Å °-0.113982942328 Å °0.300583001903 Å °0.744478895427 Å °
Refinement TLS groupSelection details: all

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