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- PDB-4zey: Crystal structure of a nuclear receptor binding factor 2 MIT doma... -

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Basic information

Entry
Database: PDB / ID: 4zey
TitleCrystal structure of a nuclear receptor binding factor 2 MIT domain (NRBF2) from Homo sapiens at 1.50 A resolution
ComponentsNuclear receptor-binding factor 2
KeywordsTRANSCRIPTION REGULATOR / Structural Genomics / Joint Center for Structural Genomics / JCSG / Partnership for Nuclear Receptor Signaling Code Biology / NHRs / PSI-BIOLOGY
Function / homology
Function and homology information


regulation of lipid kinase activity / phosphatidylinositol 3-kinase complex, class III / autophagosome / response to endoplasmic reticulum stress / transcription initiation at RNA polymerase II promoter / autophagy / Nuclear Receptor transcription pathway / cytoplasmic vesicle / nucleoplasm / cytoplasm
Similarity search - Function
Nuclear receptor-binding factor 2, C-terminal / Nuclear receptor-binding factor 2, MIT domain / Nuclear receptor-binding factor 2 / Nuclear receptor-binding factor 2, autophagy regulator / MIT domain of nuclear receptor-binding factor 2 / Phosphotransferase system, lactose/cellobiose-type IIA subunit / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Nuclear receptor-binding factor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.5 Å
AuthorsJoint Center for Structural Genomics (JCSG) / Partnership for Nuclear Receptor Signaling Code Biology (NHRS)
CitationJournal: To be published
Title: Crystal structure of a nuclear receptor binding factor 2 MIT domain (NRBF2) from Homo sapiens at 1.50 A resolution
Authors: Joint Center for Structural Genomics (JCSG) / Partnership for Nuclear Receptor Signaling Code Biology (NHRs)
History
DepositionApr 20, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Derived calculations / Refinement description ...Derived calculations / Refinement description / Source and taxonomy / Structure summary
Category: audit_author / entity_src_gen ...audit_author / entity_src_gen / pdbx_struct_oper_list / software
Item: _audit_author.name / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.3Feb 1, 2023Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nuclear receptor-binding factor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,0483
Polymers9,8561
Non-polymers1922
Water1,838102
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Nuclear receptor-binding factor 2
hetero molecules

A: Nuclear receptor-binding factor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0966
Polymers19,7122
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area2680 Å2
ΔGint-46 kcal/mol
Surface area10210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.480, 34.050, 52.340
Angle α, β, γ (deg.)90.000, 108.470, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-401-

SO4

21A-548-

HOH

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Components

#1: Protein Nuclear receptor-binding factor 2 / NRBF-2 / Comodulator of PPAR and RXR


Mass: 9855.853 Da / Num. of mol.: 1 / Fragment: UNP residues 4-86
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NRBF2, COPR / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: Q96F24
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CONSTRUCT (4-86) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED ...THE CONSTRUCT (4-86) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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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: 2.08 Å3/Da / Density % sol: 40.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 25.0% Glycerol, 1.50M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 0.95369,0.97968,0.97943
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Dec 5, 2014
Details: Vertical focusing mirror; double crystal Si(111) monochromator
RadiationMonochromator: double crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.953691
20.979681
30.979431
ReflectionResolution: 1.5→27.366 Å / Num. obs: 12873 / % possible obs: 92.4 % / Observed criterion σ(I): -3 / Redundancy: 1.685 % / Biso Wilson estimate: 17.415 Å2 / Rmerge F obs: 0.984 / Rmerge(I) obs: 0.092 / Rrim(I) all: 0.128 / Net I/σ(I): 7.56 / Num. measured all: 39652
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) allDiffraction-ID% possible all
1.5-1.550.7820.3921.83742242522340.538192.1
1.55-1.620.860.3224494285126610.43993.3
1.62-1.690.9070.2522.63697235321880.34693
1.69-1.780.920.2153.24090260524320.29793.4
1.78-1.890.9620.1534.33888251023190.21192.4
1.89-2.040.9660.1225.83937258623630.17191.4
2.04-2.240.9790.0868.63605246721930.12188.9
2.24-2.560.9580.10211.43869254223050.14390.7
2.56-3.230.9420.11115.34294258024910.15596.6
3.230.9860.05720.44036255523410.0891.6

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassification
PDB_EXTRACT3.1data extraction
SOLVEphasing
XSCALENovember 3, 2014 BUILT=20141118data scaling
BUSTER-TNT2.10.2refinement
BUSTER2.10.2refinement
XDSdata reduction
RefinementMethod to determine structure: MAD / Resolution: 1.5→27.366 Å / Cor.coef. Fo:Fc: 0.9483 / Cor.coef. Fo:Fc free: 0.9332 / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: THROUGHOUT / σ(F): 0
Details: 1. ATOM RECORDS CONTAIN SUM OF TLS AND RESIDUAL B FACTORS. 2. ANISOU RECORDS CONTAIN SUM OF TLS AND RESIDUAL U FACTORS. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE ...Details: 1. ATOM RECORDS CONTAIN SUM OF TLS AND RESIDUAL B FACTORS. 2. ANISOU RECORDS CONTAIN SUM OF TLS AND RESIDUAL U FACTORS. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. THE MAD PHASES WERE USED AS RESTRAINTS DURING REFINEMENT
RfactorNum. reflection% reflectionSelection details
Rfree0.2482 618 4.8 %RANDOM
Rwork0.2089 ---
obs0.2107 12871 97.92 %-
Displacement parametersBiso max: 89.89 Å2 / Biso mean: 25.7253 Å2 / Biso min: 11.97 Å2
Baniso -1Baniso -2Baniso -3
1-1.4756 Å20 Å20.504 Å2
2---2.3193 Å20 Å2
3---0.8436 Å2
Refine analyzeLuzzati coordinate error obs: 0.201 Å
Refinement stepCycle: LAST / Resolution: 1.5→27.366 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms679 0 10 102 791
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d357SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes21HARMONIC2
X-RAY DIFFRACTIONt_gen_planes100HARMONIC5
X-RAY DIFFRACTIONt_it702HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion85SEMIHARMONIC5
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_contact907SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d702HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg938HARMONIC20.9
X-RAY DIFFRACTIONt_omega_torsion2.49
X-RAY DIFFRACTIONt_other_torsion2.49
LS refinement shellResolution: 1.5→1.64 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.1999 144 4.7 %
Rwork0.1881 2919 -
all0.1886 3063 -
obs--97.92 %
Refinement TLS params.Method: refined / Origin x: 5.8667 Å / Origin y: 5.6877 Å / Origin z: -6.0783 Å
111213212223313233
T-0.0469 Å20.0081 Å20.0891 Å2-0.0666 Å20.0008 Å2---0.0762 Å2
L0.7284 °20.2111 °20.4411 °2-0.4439 °20.3387 °2--1.0412 °2
S0.0285 Å °0.0443 Å °0.0377 Å °-0.0622 Å °0.0025 Å °-0.0372 Å °-0.0164 Å °0.0212 Å °-0.031 Å °
Refinement TLS groupSelection details: {A|0 - 86}

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