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- PDB-7q71: The crystallographic structure of the Ligand Binding domain of th... -

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Basic information

Entry
Database: PDB / ID: 7q71
TitleThe crystallographic structure of the Ligand Binding domain of the NR7 nuclear receptor from the amphioxus Branchiostoma lanceolatum
ComponentsNuclear hormone receptor 7
KeywordsTRANSCRIPTION / Nuclear Receptor / Ligand Binding Domain / Amphioxus / Heterodimerization
Function / homology
Function and homology information


nuclear receptor activity / sequence-specific DNA binding / zinc ion binding / nucleus
Similarity search - Function
Thyroid hormone receptor / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Zinc finger, C4 type (two domains) / Nuclear hormone receptors DNA-binding domain profile. / c4 zinc finger in nuclear hormone receptors / Nuclear hormone receptor, ligand-binding domain / Nuclear hormone receptor-like domain superfamily / Ligand-binding domain of nuclear hormone receptor ...Thyroid hormone receptor / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Zinc finger, C4 type (two domains) / Nuclear hormone receptors DNA-binding domain profile. / c4 zinc finger in nuclear hormone receptors / Nuclear hormone receptor, ligand-binding domain / Nuclear hormone receptor-like domain superfamily / Ligand-binding domain of nuclear hormone receptor / Nuclear receptor (NR) ligand-binding (LBD) domain profile. / Ligand binding domain of hormone receptors / Zinc finger, NHR/GATA-type
Similarity search - Domain/homology
PHOSPHATE ION / Nuclear hormone receptor 7
Similarity search - Component
Biological speciesBranchiostoma lanceolatum (amphioxus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsBillas, I.M.L. / McEwen, A.G. / Hazemann, I. / Moras, D. / Laudet, V.
Funding support France, 4items
OrganizationGrant numberCountry
French National Research AgencyANR-2010-BLAN-1234-01 France
French National Research AgencyFRISBI ANR-10-INSB-05-01 France
French National Research AgencyANR-10-LABX-0030-INRT France
French National Research AgencyANR-10-IDEX-0002-02 France
CitationJournal: Bmc Biol. / Year: 2022
Title: A novel nuclear receptor subfamily enlightens the origin of heterodimerization.
Authors: Beinsteiner, B. / Markov, G.V. / Bourguet, M. / McEwen, A.G. / Erb, S. / Patel, A.K.M. / El Khaloufi El Khaddar, F.Z. / Lecroisey, C. / Holzer, G. / Essabri, K. / Hazemann, I. / Hamiche, A. ...Authors: Beinsteiner, B. / Markov, G.V. / Bourguet, M. / McEwen, A.G. / Erb, S. / Patel, A.K.M. / El Khaloufi El Khaddar, F.Z. / Lecroisey, C. / Holzer, G. / Essabri, K. / Hazemann, I. / Hamiche, A. / Cianferani, S. / Moras, D. / Laudet, V. / Billas, I.M.L.
History
DepositionNov 9, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 14, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 12, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 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: Nuclear hormone receptor 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,8354
Polymers26,6691
Non-polymers1663
Water1,26170
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area330 Å2
ΔGint-15 kcal/mol
Surface area11770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.290, 46.290, 163.017
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number153
Space group name H-MP3212

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Components

#1: Protein Nuclear hormone receptor 7


Mass: 26668.941 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Ligand-binding domain / Source: (gene. exp.) Branchiostoma lanceolatum (amphioxus) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A6B9UN24
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Cl
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.9 Å3/Da / Density % sol: 35.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 1.3 M Li2SO4, 0.1 M HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 8, 2013
RadiationMonochromator: Channel cut silicon monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2→40.75 Å / Num. obs: 13203 / % possible obs: 94.5 % / Redundancy: 6.4 % / Biso Wilson estimate: 47.73 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.037 / Rpim(I) all: 0.015 / Rrim(I) all: 0.04 / Net I/σ(I): 22 / Num. measured all: 85112
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2-2.056.70.96665859820.6820.3951.0461.9100
8.95-40.755.40.02102218810.0090.02268.999.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
BUSTERrefinement
XSCALEdata scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1XIU
Resolution: 2→38.93 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.947 / SU R Cruickshank DPI: 0.241 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.246 / SU Rfree Blow DPI: 0.185 / SU Rfree Cruickshank DPI: 0.185
RfactorNum. reflection% reflectionSelection details
Rfree0.235 609 4.63 %RANDOM
Rwork0.192 ---
obs0.194 13152 94.5 %-
Displacement parametersBiso max: 171.14 Å2 / Biso mean: 69.19 Å2 / Biso min: 31.81 Å2
Baniso -1Baniso -2Baniso -3
1--1.6707 Å20 Å20 Å2
2---1.6707 Å20 Å2
3---3.3414 Å2
Refine analyzeLuzzati coordinate error obs: 0.27 Å
Refinement stepCycle: final / Resolution: 2→38.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1846 0 7 70 1923
Biso mean--100.55 58.55 -
Num. residues----232
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d694SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes333HARMONIC5
X-RAY DIFFRACTIONt_it1960HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion243SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2336SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d1960HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg2666HARMONIC21.02
X-RAY DIFFRACTIONt_omega_torsion2.7
X-RAY DIFFRACTIONt_other_torsion18.74
LS refinement shellResolution: 2→2.02 Å / Rfactor Rfree error: 0 / Total num. of bins used: 30
RfactorNum. reflection% reflection
Rfree0.3032 29 6.61 %
Rwork0.2266 410 -
all0.2316 439 -
obs--99.3 %
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)
10.2326-0.92280.20433.9297-2.51091.17560.1442-0.0051-0.0523-0.0912-0.156-0.03760.1595-0.08170.01170.11250.28610.0422-0.1125-0.0768-0.1681-6.1599-29.544314.3743
24.8208-2.37450.24583.1787-1.66671.95920.0778-0.30520.0658-0.0357-0.2912-0.03630.41310.01010.2134-0.13490.0946-0.0102-0.0560.0076-0.1302-12.3237-12.04226.044
3-0.49-0.2167-2.563.0556-1.38681.57550.01330.0030.1125-0.074-0.0235-0.1151-0.1014-0.03720.0102-0.10440.09330.07520.0094-0.06650.304-22.88976.887630.2517
48.75630.4487-2.14875.4386-2.09915.23420.17250.12510.1068-0.1872-0.6554-0.56680.13120.70420.4829-0.14210.10770.03510.08450.1620.0411-1.4202-6.301818.9966
53.1183-0.8305-0.75141.5508-0.89772.84760.10320.23610.216-0.2217-0.1747-0.10030.0539-0.20230.0715-0.10490.11010.0109-0.067-0.0033-0.12-18.4302-7.288717.9494
67.4052-0.78923.97571.5951-1.06536.6639-0.01630.61960.5124-0.3418-0.02990.1854-0.00740.07920.04620.24370.08160.03330.2020.062-0.1987-23.971-4.364911.1058
72.0140.68211.11713.69680.46674.98930.11140.63840.0801-0.45010.0027-0.58220.24110.6709-0.11420.02040.33920.1555-0.02040.0347-0.2404-3.7999-15.86286.7526
8-1.16440.8911-3.66643.89810.52957.77290.06940.16740.2219-0.193-0.08050.0630.37750.04870.01110.21690.2258-0.1421-0.2169-0.0195-0.304-13.5566-18.81852.2113
90.5468-0.670.26681.84120.02160.10340.01170.02010.0164-0.0098-0.0198-0.0111-0.0242-0.00680.00810.20570.0114-0.04930.0758-0.09890.1158-13.32725.546211.4783
101.12341.29440.44511.9651.49720.84010.003-0.0473-0.14630.00280.0167-0.0869-0.12720.0126-0.0198-0.1539-0.07340.03630.0680.0808-0.02241.68961.791921.9871
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|158 - A|167 }A158 - 167
2X-RAY DIFFRACTION2{ A|168 - A|189 }A168 - 189
3X-RAY DIFFRACTION3{ A|190 - A|202 }A190 - 202
4X-RAY DIFFRACTION4{ A|203 - A|232 }A203 - 232
5X-RAY DIFFRACTION5{ A|233 - A|270 }A233 - 270
6X-RAY DIFFRACTION6{ A|271 - A|294 }A271 - 294
7X-RAY DIFFRACTION7{ A|295 - A|340 }A295 - 340
8X-RAY DIFFRACTION8{ A|341 - A|360 }A341 - 360
9X-RAY DIFFRACTION9{ A|361 - A|378 }A361 - 378
10X-RAY DIFFRACTION10{ A|379 - A|389 }A379 - 389

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