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- PDB-3u21: Crystal structure of a Fragment of Nuclear factor related to kapp... -

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Basic information

Entry
Database: PDB / ID: 3u21
TitleCrystal structure of a Fragment of Nuclear factor related to kappa-B-binding protein (residues 370-495) (NFRKB) from Homo sapiens at 2.18 A resolution
ComponentsNuclear factor related to kappa-B-binding protein
KeywordsTranscription regulation / DNA BINDING / DNA/RNA-binding 3-helical bundle / winged-HTH domain / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY / DNA BINDING PROTEIN / Partnership for Stem Cell Biology / STEMCELL
Function / homology
Function and homology information


regulation of DNA strand elongation / positive regulation of telomere maintenance in response to DNA damage / Ino80 complex / regulation of chromosome organization / regulation of DNA replication / regulation of embryonic development / regulation of DNA repair / positive regulation of DNA repair / telomere maintenance / DNA Damage Recognition in GG-NER ...regulation of DNA strand elongation / positive regulation of telomere maintenance in response to DNA damage / Ino80 complex / regulation of chromosome organization / regulation of DNA replication / regulation of embryonic development / regulation of DNA repair / positive regulation of DNA repair / telomere maintenance / DNA Damage Recognition in GG-NER / UCH proteinases / DNA recombination / protease binding / regulation of cell cycle / chromatin remodeling / DNA repair / positive regulation of DNA-templated transcription / DNA binding / nucleoplasm / nucleus
Similarity search - Function
NFRKB winged helix-like domain / Nuclear factor related to kappa-B-binding protein / NFRKB winged helix-like domain / NFRKB winged helix-like domain superfamily / NFRKB Winged Helix-like / DEUBAD domain / DEUBAD (DEUBiquitinase ADaptor) domain profile. / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Nuclear factor related to kappa-B-binding protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.18 Å
AuthorsJoint Center for Structural Genomics (JCSG) / Partnership for Stem Cell Biology / Partnership for Stem Cell Biology (STEMCELL)
CitationJournal: Plos One / Year: 2012
Title: Structure of a Novel Winged-Helix Like Domain from Human NFRKB Protein.
Authors: Kumar, A. / Mocklinghoff, S. / Yumoto, F. / Jaroszewski, L. / Farr, C.L. / Grzechnik, A. / Nguyen, P. / Weichenberger, C.X. / Chiu, H.J. / Klock, H.E. / Elsliger, M.A. / Deacon, A.M. / ...Authors: Kumar, A. / Mocklinghoff, S. / Yumoto, F. / Jaroszewski, L. / Farr, C.L. / Grzechnik, A. / Nguyen, P. / Weichenberger, C.X. / Chiu, H.J. / Klock, H.E. / Elsliger, M.A. / Deacon, A.M. / Godzik, A. / Lesley, S.A. / Conklin, B.R. / Fletterick, R.J. / Wilson, I.A.
History
DepositionSep 30, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 2, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 10, 2012Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Feb 1, 2023Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nuclear factor related to kappa-B-binding protein
B: Nuclear factor related to kappa-B-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0313
Polymers29,0082
Non-polymers231
Water45025
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1510 Å2
ΔGint-23 kcal/mol
Surface area11610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.942, 60.942, 130.839
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A372 - 437
2114B372 - 437
1214A445 - 483
2214B445 - 483
DetailsCRYSTAL PACKING ANALYSIS SUGGESTS THE ASSIGNMENT OF A DIMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein Nuclear factor related to kappa-B-binding protein / DNA-binding protein R kappa-B / INO80 complex subunit G


Mass: 14504.097 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BC063280, INO80G, NFRKB / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q6P4R8
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 25 / Source method: isolated from a natural source / Formula: H2O
Sequence details1. THIS CONSTRUCT (RESIDUES 370-495) WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG ...1. THIS CONSTRUCT (RESIDUES 370-495) WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE. RESIDUE NUMBERING IS BASED ON ISOFORM 1 OF UNIPROTKB ID Q6P4R8. 2. THE PROTEIN WAS REDUCTIVELY METHYLATED PRIOR TO CRYSTALLIZATION.

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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: 2.09 Å3/Da / Density % sol: 41.26 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.09M HEPES pH 7.5, 10% glycerol, 1.26M tri-sodium citrate, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91837,0.97936,0.97915
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 22, 2011 / Details: double crystal monochromator
RadiationMonochromator: double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979361
30.979151
ReflectionResolution: 2.18→35.466 Å / Num. obs: 13560 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 41.259 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 20.78
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.18-2.260.7962.49710136099.9
2.26-2.350.6243.19264129899.8
2.35-2.450.5063.889391247100
2.45-2.580.3655.394881332100
2.58-2.750.2487.9100061409100
2.75-2.960.15212.293681322100
2.96-3.250.10118.193001316100
3.25-3.720.04735.29515136999.9
3.72-4.680.02953.29606140799.9
4.680.02458.99421150098.3

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
XSCALEDecember 6, 2010data scaling
REFMAC5.6.0116refinement
XDSdata reduction
SHELXDphasing
RefinementMethod to determine structure: MAD / Resolution: 2.18→35.466 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.905 / Occupancy max: 1 / Occupancy min: 0.37 / SU B: 12.518 / SU ML: 0.156 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.222
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 5. 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. 6. SODIUM ION (NA) FROM CRYSTALLIZATION CONDITION WAS MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.2695 662 4.9 %RANDOM
Rwork0.2305 ---
obs0.2324 13504 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 97.07 Å2 / Biso mean: 46.2329 Å2 / Biso min: 25.43 Å2
Baniso -1Baniso -2Baniso -3
1--0.21 Å20 Å20 Å2
2---0.21 Å20 Å2
3---0.43 Å2
Refinement stepCycle: LAST / Resolution: 2.18→35.466 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1732 0 1 25 1758
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221780
X-RAY DIFFRACTIONr_bond_other_d0.0010.021163
X-RAY DIFFRACTIONr_angle_refined_deg1.2521.9782425
X-RAY DIFFRACTIONr_angle_other_deg0.86632861
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4825214
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.30826.10477
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.03715.133301
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.053152
X-RAY DIFFRACTIONr_chiral_restr0.070.2279
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211922
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02338
X-RAY DIFFRACTIONr_bond_it2.7823.8951780
X-RAY DIFFRACTIONr_bond_other0.4783.9171163
X-RAY DIFFRACTIONr_angle_it4.1768.6432424
X-RAY DIFFRACTIONr_angle_others2.4488.8252861
X-RAY DIFFRACTIONr_torsion_it6.82417.777594
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 1360 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
MEDIUM POSITIONAL0.230.5
MEDIUM THERMAL2.312
LS refinement shellResolution: 2.18→2.236 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 40 -
Rwork0.252 809 -
all-849 -
obs--99.88 %
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)
11.06350.6754-0.20695.42840.17364.0382-0.09250.03210.1089-0.05770.1532-0.2375-0.35290.0032-0.06070.104-0.0072-0.01810.0908-0.01910.0861.03845.34153.345
23.08640.5889-0.53432.0962-0.38844.42760.0515-0.2075-0.05910.01710.10510.14580.0318-0.504-0.15660.09910.0091-0.03050.16360.04870.050948.69130.99275.432
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A372 - 462
2X-RAY DIFFRACTION1A466 - 483
3X-RAY DIFFRACTION2B370 - 461
4X-RAY DIFFRACTION2B464 - 483

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