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- PDB-8ar6: Structure of Delta 57-NCOA7 in space group P41212 -

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Basic information

Entry
Database: PDB / ID: 8ar6
TitleStructure of Delta 57-NCOA7 in space group P41212
ComponentsNuclear receptor coactivator 7
KeywordsANTIVIRAL PROTEIN / human NCOA7 / viral restriction factors
Function / homology
Function and homology information


negative regulation of cellular response to oxidative stress / nuclear receptor binding / response to oxidative stress / transcription coactivator activity / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleus
Similarity search - Function
TLDc domain / TLDc domain / TLDc domain profile. / domain in TBC and LysM domain containing proteins / Lysin motif / LysM domain superfamily / LysM domain / LysM domain profile. / LysM domain
Similarity search - Domain/homology
Nuclear receptor coactivator 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsCampeotto, I. / Foster, T.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust217414/Z/19/Z United Kingdom
CitationJournal: Iucrj / Year: 2023
Title: Protein-to-structure pipeline for ambient-temperature in situ crystallography at VMXi.
Authors: Mikolajek, H. / Sanchez-Weatherby, J. / Sandy, J. / Gildea, R.J. / Campeotto, I. / Cheruvara, H. / Clarke, J.D. / Foster, T. / Fujii, S. / Paulsen, I.T. / Shah, B.S. / Hough, M.A.
History
DepositionAug 15, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 24, 2023Provider: repository / Type: Initial release
Revision 1.1May 31, 2023Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jul 19, 2023Group: Data collection / Database references / Category: citation / citation_author / diffrn_source
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _diffrn_source.pdbx_synchrotron_site
Revision 1.3Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / diffrn_source / pdbx_initial_refinement_model
Item: _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nuclear receptor coactivator 7
B: Nuclear receptor coactivator 7
C: Nuclear receptor coactivator 7


Theoretical massNumber of molelcules
Total (without water)62,4433
Polymers62,4433
Non-polymers00
Water3,369187
1
A: Nuclear receptor coactivator 7


Theoretical massNumber of molelcules
Total (without water)20,8141
Polymers20,8141
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Nuclear receptor coactivator 7


Theoretical massNumber of molelcules
Total (without water)20,8141
Polymers20,8141
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Nuclear receptor coactivator 7


Theoretical massNumber of molelcules
Total (without water)20,8141
Polymers20,8141
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.623, 89.623, 165.897
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein Nuclear receptor coactivator 7 / 140 kDa estrogen receptor-associated protein / Estrogen nuclear receptor coactivator 1


Mass: 20814.289 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NCOA7, ERAP140, ESNA1, Nbla00052, Nbla10993 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8NI08
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 187 / Source method: isolated from a natural source / Formula: H2O

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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: 2.67 Å3/Da / Density % sol: 53.89 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2 M di ammonium hydrogen citrate, 20% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: May 18, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.2→60.88 Å / Num. obs: 34845 / % possible obs: 99.12 % / Redundancy: 6.7 % / Biso Wilson estimate: 39.78 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.07686 / Rpim(I) all: 0.03128 / Net I/σ(I): 18.72
Reflection shellResolution: 2.2→2.279 Å / Rmerge(I) obs: 0.704 / Num. unique obs: 3402 / CC1/2: 0.697 / Rpim(I) all: 0.2945

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Processing

Software
NameVersionClassification
Aimless1.20.1_4487data scaling
PHENIX1.20.1_4487refinement
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ACJ

4acj


Resolution: 2.2→60.88 Å / SU ML: 0.2842 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.0864
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2384 1719 4.94 %
Rwork0.1913 33083 -
obs0.1936 34802 99.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 51.32 Å2
Refinement stepCycle: LAST / Resolution: 2.2→60.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4122 0 0 187 4309
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00224245
X-RAY DIFFRACTIONf_angle_d0.49975746
X-RAY DIFFRACTIONf_chiral_restr0.0383590
X-RAY DIFFRACTIONf_plane_restr0.0034737
X-RAY DIFFRACTIONf_dihedral_angle_d4.9852560
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.260.37991490.31512690X-RAY DIFFRACTION99.02
2.26-2.340.25871320.25562709X-RAY DIFFRACTION99.93
2.34-2.420.26851410.21512756X-RAY DIFFRACTION100
2.42-2.520.2641450.21672722X-RAY DIFFRACTION99.9
2.52-2.630.26411410.22432755X-RAY DIFFRACTION99.9
2.63-2.770.281430.23692723X-RAY DIFFRACTION99.65
2.77-2.950.29951350.22942759X-RAY DIFFRACTION99.79
2.95-3.170.21991480.20152720X-RAY DIFFRACTION98.46
3.17-3.490.22071510.18482764X-RAY DIFFRACTION99.35
3.49-40.2311220.17572801X-RAY DIFFRACTION99.22
4-5.040.20281500.14642773X-RAY DIFFRACTION97.63
5.04-60.880.2271620.17852911X-RAY DIFFRACTION96.94
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)
12.31922397589-0.8863059354531.01578108522.84864812589-0.3772304447972.9364108819-0.123557718814-0.2483735280350.1094409711770.2896826123990.184431753383-0.140407812498-0.140470072759-0.0488441373603-0.0624413253010.2867147179350.0318550027704-0.02740043881330.201947063312-0.02495991826230.26541517373932.866320247892.616048118634.1515621765
23.87442903837-0.322031450308-0.07812431193533.03289030469-0.2591560759552.086928928780.08958315815190.350927743868-0.0367013958209-0.455941344047-0.0709998171031-0.121065558450.1216518760.165238779835-0.007586270262020.2853913347380.0605912718827-0.00947177115110.280423803826-0.01109643607020.22942956025456.423186888572.276037573544.7818645496
32.592216430870.4656693965870.02707986436684.213548636050.1989407885412.75894005040.164352876471-0.300879991271-0.752430200310.560764912899-0.234341501633-0.2617627973461.13460768031-0.02708444720110.08742189306310.77606952838-0.0513071033124-0.0787356521260.3356978784430.04490994388950.5128106983846.327380880545.255713228863.755943576
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain A and resseq 13:183)AA13 - 1831 - 171
22(chain B and resseq 12:183)BB12 - 1831 - 172
33(chain C and resseq 15:183)CC15 - 1831 - 169

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