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- PDB-7obp: Crystal structure of the human NCOA7-AS TLDc domain -

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Basic information

Entry
Database: PDB / ID: 7obp
TitleCrystal structure of the human NCOA7-AS TLDc domain
ComponentsNCOA7-AS
KeywordsANTIVIRAL PROTEIN / NCOA7 / TLDc domain / V-ATPase binding partner
Function / homologyTLDc domain profile. / TLDc domain / TLD / domain in TBC and LysM domain containing proteins / NCOA7-AS
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsBlaise, M.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-20-CE15-0010-02 France
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2021
Title: Crystal structure of the TLDc domain of human NCOA7-AS.
Authors: Arnaud-Arnould, M. / Tauziet, M. / Moncorge, O. / Goujon, C. / Blaise, M.
History
DepositionApr 23, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 14, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 4, 2021Group: Database references / Category: citation
Item: _citation.journal_id_CSD / _citation.pdbx_database_id_DOI / _citation.title
Revision 1.2Sep 29, 2021Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Jan 31, 2024Group: 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: NCOA7-AS
B: NCOA7-AS
C: NCOA7-AS
D: NCOA7-AS
E: NCOA7-AS
F: NCOA7-AS


Theoretical massNumber of molelcules
Total (without water)115,0776
Polymers115,0776
Non-polymers00
Water19,7981099
1
A: NCOA7-AS


Theoretical massNumber of molelcules
Total (without water)19,1801
Polymers19,1801
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: NCOA7-AS


Theoretical massNumber of molelcules
Total (without water)19,1801
Polymers19,1801
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: NCOA7-AS


Theoretical massNumber of molelcules
Total (without water)19,1801
Polymers19,1801
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: NCOA7-AS


Theoretical massNumber of molelcules
Total (without water)19,1801
Polymers19,1801
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: NCOA7-AS


Theoretical massNumber of molelcules
Total (without water)19,1801
Polymers19,1801
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: NCOA7-AS


Theoretical massNumber of molelcules
Total (without water)19,1801
Polymers19,1801
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.410, 107.060, 146.440
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein
NCOA7-AS


Mass: 19179.508 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NCOA7 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: H0Y5F6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1099 / 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: 2.2 Å3/Da / Density % sol: 47.21 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.5 / Details: 0.1 M sodium acetate pH4.5, 30% PEG 300

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.965 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Mar 12, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.965 Å / Relative weight: 1
ReflectionResolution: 1.8→45.29 Å / Num. obs: 100055 / % possible obs: 99.7 % / Redundancy: 5.2 % / Biso Wilson estimate: 19.8 Å2 / CC1/2: 0.997 / Rrim(I) all: 0.1473 / Net I/σ(I): 10.1
Reflection shellResolution: 1.8→1.86 Å / Num. unique obs: 9863 / CC1/2: 0.58 / Rrim(I) all: 1.14

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4acj
Resolution: 1.8→45.29 Å / SU ML: 0.2221 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.0355
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2212 2000 2 %
Rwork0.1766 98034 -
obs0.1774 100034 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.89 Å2
Refinement stepCycle: LAST / Resolution: 1.8→45.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7982 0 0 1106 9088
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00528421
X-RAY DIFFRACTIONf_angle_d0.786111433
X-RAY DIFFRACTIONf_chiral_restr0.05051177
X-RAY DIFFRACTIONf_plane_restr0.00641475
X-RAY DIFFRACTIONf_dihedral_angle_d11.95112984
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.850.36421410.28376939X-RAY DIFFRACTION99.77
1.85-1.890.27671410.24636892X-RAY DIFFRACTION99.83
1.89-1.950.22451420.22146954X-RAY DIFFRACTION99.93
1.95-2.010.22161420.20256932X-RAY DIFFRACTION99.96
2.01-2.090.25261410.19146947X-RAY DIFFRACTION99.94
2.09-2.170.20341410.18316922X-RAY DIFFRACTION99.94
2.17-2.270.25921420.18366991X-RAY DIFFRACTION99.89
2.27-2.390.24111430.18226957X-RAY DIFFRACTION99.73
2.39-2.540.21931420.18096959X-RAY DIFFRACTION99.64
2.54-2.730.24291420.18296994X-RAY DIFFRACTION99.72
2.73-3.010.24871440.17937011X-RAY DIFFRACTION99.86
3.01-3.440.20561440.16497077X-RAY DIFFRACTION99.92
3.44-4.340.19891450.14147115X-RAY DIFFRACTION99.85
4.34-45.290.181500.16187344X-RAY DIFFRACTION99.34
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
14.147671356340.05516418382962.419038242335.099164790351.555864280234.64331580951-0.14382352179-0.09334468331520.8394112113060.0633134670665-0.1680256035690.464776583868-1.07386107454-0.7491137519280.206510642440.3350491537580.1128831805870.03756045663070.2765807335090.004319888730640.3291668374172.055014404224.7790513181-18.4929017861
21.584431333750.2337526169580.3071543040611.085642600370.1494752943291.360964590340.0210753377818-0.01853035041550.110046792501-0.0378943276049-0.02972127759480.0787484559026-0.142709447374-0.0652356902172-0.006503575690180.1186543742040.00903425724155-0.004718804242620.0802531745471-0.006965429083940.096088615126511.908706715515.6391227824-22.221165615
32.631684646660.472799466391.899040348071.699823598540.034515234922.73561483371-0.1086813181240.2721726906510.245367284427-0.2394371820590.0255490020897-0.106043111573-0.2485583573010.2351330878120.05589433772950.191396712868-0.01324737475870.01377580565260.1549934414920.005568297116580.14385148438719.09125320919.2721048729-31.8927630701
45.694293938584.57491051469-1.064176587994.38588603722-0.8545988431881.220475429680.115628543847-0.122547578478-0.02025882510840.137596523227-0.11818517466-0.0462714265345-0.08439677519940.03039001333750.01107203689680.1512608771550.0201794829722-0.01625904284850.0885559825041-0.009071171844240.11493117258714.243829385620.094859843-18.5114507634
53.79938234046-1.10057306345-3.189332968484.28936940663.478647707524.77543741436-0.193795625745-0.189236404496-1.068348511650.576900425307-0.1724076005530.200984330841.09524676532-0.1888092151480.2964435507360.320884503284-0.0163097133122-0.03099745219940.2145453126370.03860755276910.433158384311.27768235389-26.8834111645-20.8745864725
61.828629684080.267277449335-0.07404530894321.100763785540.03172692708111.278038338160.02266873831870.0289712089264-0.1179653026340.00130335545806-0.01507748873640.001045483736760.0463255650773-0.0570488814107-0.008270009999330.1012343612320.00268910765348-0.02233886197590.0871420197759-0.01261447786630.1156384643820.87988545679-11.8374896448-25.178897895
72.38826546860.3347248363113.774597147162.91335143207-0.7378497111686.84926746032-0.2430874746310.36733988830.393287830714-0.4568222555290.0502679638714-0.0629627721364-1.464712665080.3428438825040.1757667421540.419081831976-0.0200922588270.03472098564620.2448718657370.04045723295810.2550479686579.3237297223430.10952782914.10337326709
81.42400860548-0.308216704622-0.1724801947191.090518524760.3130097661721.655307191520.0326203323974-0.004384725539960.0221877524935-0.00458963279327-0.004870934712490.0399766313334-0.0707949920232-0.174911980959-0.02205712205710.1353199350450.009685796080050.002518852158680.1365279583220.01898119254420.09574259268995.039997925415.57357094389.03714889384
95.927970503760.8471821355482.550684158497.5801703565-5.808044676947.75135988975-0.231855865549-0.4719108874630.3046129458070.5531752186680.0535497926769-0.389163776606-0.6313836059950.5889302727630.1173132910810.2106672326050.0447125593649-0.01364148165040.343027551967-0.1206901017480.30278174137246.3767167-1.38470881241-21.3248058758
102.904331980540.603682441411-0.4872950315284.2076133852-1.143302355092.762795352610.0274166999616-0.3812643833640.3364124857140.582089726319-0.0916304825815-0.413744444796-0.2767017972290.3172498184430.0785675541550.1696181716950.0386921318186-0.05113828771510.285257654601-0.07037466781660.22486581384534.7290965592-1.42509472038-18.7893057248
111.97126489037-0.230102996757-0.1366029785250.8656981388470.06731882974610.873997881547-0.0288294007303-0.186675812717-0.06971856425830.06072027122140.0351824082539-0.04358119920190.02369339875190.119454643998-0.01279731045510.1006175625420.0309564281945-0.02004336851750.125005764588-0.0133343454240.11847535783530.4980786024-7.04975212669-25.0268198167
123.16363952347-0.330896115399-0.9157537551690.31034969674-0.4565176762371.57948558835-0.0216284987580.156068181984-0.241913077268-0.0872536129585-0.00626485753871-0.003142716798320.0311634519061-0.01200236690950.02686992518180.1546405717160.015945780655-0.01275598895470.144201505196-0.0401699433890.14851216895832.4388972793-10.1835754241-34.5946489022
132.96646306074-0.0731778174056-1.027602980512.48593750766-1.402531789523.82838888114-0.1560128484180.0580909521158-0.44364544862-0.09210546893220.0540930184143-0.07745188710730.1633970382410.1033824080580.07572011262370.1288654880220.0322373085054-0.01495225721080.136347358828-0.03576875858760.20208358485435.4329844244-16.640112687-31.9599983007
142.90558842752-0.938876938320.5026550183815.183830303920.6930476735682.00336222963-0.229389166774-0.586002681881-0.05997868979970.3358885645730.227856178407-0.2012726782150.08683731634550.1731674612430.03729472622420.1134613400620.0455016002792-0.01168468397420.2776350897320.01624313632760.16801811110736.4070808999-9.8183619982-20.5138244314
156.206640473481.67932903662-4.099017940812.52430031757-3.829054397677.783982589940.2745580536721.02437798372-0.586652971377-0.478550296409-0.247873511311-0.8413310624130.863674743471.208815856820.01104877805420.4991505043960.259700827716-0.02822122728020.759612370714-0.1101657932630.54745112160446.1787867762-5.693267555225.70512592621
162.43588292669-0.6808969265250.5970558563721.14187104498-0.3282230272741.607038571120.2636832156450.556000093142-0.237355661125-0.226370948596-0.159128089323-0.0843939824090.255559399340.498148099725-0.08810508039980.2183128242230.0620583019327-0.03731259273040.291666599032-0.02955714983220.17890387119233.19288669861.37857857956.84419792029
174.24727971452-1.315781786610.5985054024062.85218024686-0.3952120108511.77547149170.1065591974010.02182840093320.1540588000860.0443316132811-0.0313674992644-0.1910169207410.1169299932880.460905278781-0.08456536347460.156683666074-0.013752438498-0.02983388391130.214734354987-0.01254340163730.14218526594835.18301931475.5560647595318.4465134681
182.90858590871-0.2959049400450.3826102967382.01002419785-0.6608896832992.115514345470.009482252897980.605671110380.26054610168-0.041778301892-0.120081357847-0.152051883983-0.2990213460280.7727985809190.03301429490160.196400835624-0.0510602827887-0.04939890267040.391046792610.0595035157630.22435548527939.06505858219.1287682794511.4245109408
192.19882369837-1.45599388502-0.7836169349971.150334985621.082439676052.004964487280.274167719979-0.46132072457-1.04083325150.268277540437-0.2523432072210.3218350181510.917862117474-0.7288708299240.07297544759810.940468720694-0.39077760305-0.2233892641310.6196219142090.1281477349150.536781331348-3.3115702663-20.38878392832.63138542112
201.88857630939-0.1165990225580.2696458086630.8811196166180.009081357609492.578112934960.466691923619-0.00273634041074-0.3693841017670.270005300942-0.150551661423-0.004455405789280.794951086583-0.447136020897-0.2295784943530.351674595145-0.0691787447182-0.1292367543760.333473858048-0.0469840656690.310912840714.61933942039-11.56655389110.399768408413
211.399563750980.362752371446-0.6724998124162.50243440440.151153194130.3771408699430.3920103090650.115846129548-0.4785227172760.1103210909850.0336247267528-0.1572919413860.65147460012-0.0608567298808-0.2217624832670.40877382335-0.0401338085859-0.1692608013520.22677486695-0.03370605529370.25544853584512.4476402812-11.17112183021.89337039158
221.094735297930.357938226533-0.424419361771.183935695470.8042044130011.16411540120.179577753480.118264622995-0.706552004579-0.01245053777030.0240261020204-0.1231891455850.63227547791-0.0158439696018-0.01370693360440.815866216289-0.254999384085-0.3774676759650.2365675571710.08815621588080.6406468389337.42867328907-23.92925443796.48864166557
235.164806187520.1797291348921.45142788030.209203370322-0.1983970093071.163352679980.329310802697-0.253455231056-0.2906156341780.171444944341-0.0488005175031-0.3003038277170.505104017233-0.119167871607-0.2479934675840.335953644608-0.0643054405773-0.09948877888420.1645966143730.02695963574110.25264190959916.6128553144-6.7042404966811.445590921
240.9719974611560.557795432831-0.4028508572520.453715783138-0.2658395571060.1744821236280.0518084064013-0.026597156381-0.20638334395-0.0374148441060.03418145311960.1630958451770.331912232522-0.241018423907-0.005349149379060.567360560856-0.343908281262-0.1455534670620.3033967136750.1733007642730.2870925349446.38312205485-12.974242753314.0863726433
251.384741827490.2748977510910.2853673799080.0935185510865-0.06218906170990.967069771380.530850362582-0.206489632438-0.7615573829780.222190159847-0.092456078243-0.05170415442170.72099900038-0.1809732873470.07574163975540.745707180857-0.117205275504-0.3449211311160.260943120350.104428670070.51817858033514.159710162-17.740368604913.6734756951
261.06298729976-0.329753270689-0.06806234292172.9974299806-1.823043871651.773372249760.0511774133485-0.0668941946475-0.362564854862-0.204970483840.01291534811690.05180975943130.499038820026-0.0606475789436-0.2525273579760.840715617477-0.203186856081-0.3047941644030.373453677720.2650172559760.44397473540110.855545662-24.531693506717.6388793538
270.758694133596-0.360834861247-0.5118644039871.10831390968-0.1561007226120.5198120013550.264670411762-0.0405295688558-0.5329420123350.436980163627-0.0135004940716-0.2946123906680.7767099954040.0308826439647-0.1324620301650.644231473249-0.0344284735826-0.2620653564820.246629497507-0.03751549421940.4612662647469.51258005513-18.69352273841.83450194155
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 54 through 71 )AA54 - 711 - 18
22chain 'A' and (resid 72 through 152 )AA72 - 15219 - 99
33chain 'A' and (resid 153 through 206 )AA153 - 206100 - 152
44chain 'A' and (resid 207 through 219 )AA207 - 219153 - 165
55chain 'B' and (resid 55 through 71 )BB55 - 711 - 17
66chain 'B' and (resid 72 through 219 )BB72 - 21918 - 165
77chain 'C' and (resid 55 through 71 )CC55 - 711 - 17
88chain 'C' and (resid 72 through 219 )CC72 - 21918 - 165
99chain 'D' and (resid 55 through 71 )DD55 - 711 - 17
1010chain 'D' and (resid 72 through 93 )DD72 - 9318 - 39
1111chain 'D' and (resid 94 through 144 )DD94 - 14440 - 90
1212chain 'D' and (resid 145 through 179 )DD145 - 17991 - 125
1313chain 'D' and (resid 180 through 206 )DD180 - 206126 - 152
1414chain 'D' and (resid 207 through 219 )DD207 - 219153 - 165
1515chain 'E' and (resid 55 through 71 )EE55 - 711 - 17
1616chain 'E' and (resid 72 through 144 )EE72 - 14418 - 90
1717chain 'E' and (resid 145 through 179 )EE145 - 17991 - 125
1818chain 'E' and (resid 180 through 219 )EE180 - 219126 - 165
1919chain 'F' and (resid 55 through 71 )FF55 - 711 - 17
2020chain 'F' and (resid 72 through 93 )FF72 - 9318 - 39
2121chain 'F' and (resid 94 through 114 )FF94 - 11440 - 60
2222chain 'F' and (resid 115 through 124 )FF115 - 12461 - 70
2323chain 'F' and (resid 125 through 134 )FF125 - 13471 - 80
2424chain 'F' and (resid 135 through 144 )FF135 - 14481 - 90
2525chain 'F' and (resid 145 through 190 )FF145 - 19091 - 130
2626chain 'F' and (resid 191 through 206 )FF191 - 206131 - 146
2727chain 'F' and (resid 207 through 219 )FF207 - 219147 - 159

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