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- PDB-3qve: Crystal structure of human HMG box-containing protein 1, HBP1 -

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Basic information

Entry
Database: PDB / ID: 3qve
TitleCrystal structure of human HMG box-containing protein 1, HBP1
ComponentsHMG box-containing protein 1
KeywordsTRANSCRIPTION / SGC / HMG box transcription factor 1 / HBP1 / AXH domain / Structural Genomics Consortium
Function / homology
Function and homology information


Wnt signaling pathway / DNA-binding transcription factor activity, RNA polymerase II-specific / regulation of cell cycle / nuclear speck / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin / regulation of transcription by RNA polymerase II / RNA binding / nucleoplasm / nucleus
Similarity search - Function
HMG box-containing protein 1 / Ataxin, AXH domain / Ataxin, AXH domain superfamily / Ataxin-1 and HBP1 module (AXH) / AXH domain profile. / domain in Ataxins and HMG containing proteins / HMG (high mobility group) box / HMG boxes A and B DNA-binding domains profile. / high mobility group / High mobility group box domain / High mobility group box domain superfamily
Similarity search - Domain/homology
HMG box-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04 Å
AuthorsChaikuad, A. / Krysztofinska, E. / Cocking, R. / Vollmar, M. / Yue, W.W. / Krojer, T. / Ugochukwu, E. / Filippakopoulos, P. / von Delft, F. / Arrowsmith, C.H. ...Chaikuad, A. / Krysztofinska, E. / Cocking, R. / Vollmar, M. / Yue, W.W. / Krojer, T. / Ugochukwu, E. / Filippakopoulos, P. / von Delft, F. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A.M. / Bountra, C. / Oppermann, U. / Structural Genomics Consortium / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal structure of human HMG box-containing protein 1, HBP1
Authors: Chaikuad, A. / Krysztofinska, E. / Cocking, R. / Vollmar, M. / Yue, W.W. / Krojer, T. / Ugochukwu, E. / Filippakopoulos, P. / von Delft, F. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A.M. / ...Authors: Chaikuad, A. / Krysztofinska, E. / Cocking, R. / Vollmar, M. / Yue, W.W. / Krojer, T. / Ugochukwu, E. / Filippakopoulos, P. / von Delft, F. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A.M. / Bountra, C. / Oppermann, U. / Structural Genomics Consortium
History
DepositionFeb 25, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / 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 / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_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: HMG box-containing protein 1
B: HMG box-containing protein 1
C: HMG box-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,92641
Polymers46,4653
Non-polymers2,46138
Water7,134396
1
A: HMG box-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,32914
Polymers15,4881
Non-polymers84113
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: HMG box-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,57818
Polymers15,4881
Non-polymers1,08917
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: HMG box-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,0199
Polymers15,4881
Non-polymers5318
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)118.840, 118.840, 93.190
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-70-

HOH

21A-385-

HOH

31B-111-

HOH

41B-128-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
31B

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11TRPTRPPHEPHE5AA207 - 3124 - 109
21TRPTRPPHEPHE5CC207 - 3124 - 109
31TRPTRPPHEPHE5BB207 - 3124 - 109
12TYRTYRCYSCYS6AA313 - 326110 - 123
22TYRTYRCYSCYS6CC313 - 326110 - 123
32TYRTYRCYSCYS6BB313 - 326110 - 123
13GLUGLUPROPRO5AA327 - 337124 - 134
23GLUGLUPROPRO5CC327 - 337124 - 134
33GLUGLUPROPRO5BB327 - 337124 - 134

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Components

#1: Protein HMG box-containing protein 1 / HMG box transcription factor 1 / High mobility group box transcription factor 1


Mass: 15488.395 Da / Num. of mol.: 3 / Fragment: AXH domain residues 206-342
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HBP1 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-R3-pRARE2 / References: UniProt: O60381
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 35 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 396 / 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: 4.09 Å3/Da / Density % sol: 69.91 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 25% PEG 3350, 0.3M Ammonium sulfate, 0.1M Bis-Tris, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 277.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: ADSC Q315 3x3 CCD / Detector: CCD / Date: Jun 30, 2010 / Details: Kirkpatrick Baez bimorph mirror pair
RadiationMonochromator: Si (111) double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.04→59.42 Å / Num. all: 48373 / Num. obs: 48353 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.7 % / Biso Wilson estimate: 33.9 Å2 / Rmerge(I) obs: 0.097 / Net I/σ(I): 11.1
Reflection shellResolution: 2.04→2.15 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.757 / Mean I/σ(I) obs: 2.1 / Num. unique all: 6798 / % possible all: 97.1

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Processing

Software
NameVersionClassification
GDAdata collection
PHASERphasing
REFMAC5.5.0110refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1V06

1v06


Resolution: 2.04→35.9 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.955 / SU B: 4.986 / SU ML: 0.071 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2 / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19175 2051 4.2 %RANDOM
Rwork0.16243 ---
obs0.1637 46301 99.4 %-
all-48353 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.142 Å2
Baniso -1Baniso -2Baniso -3
1--0.69 Å2-0.35 Å20 Å2
2---0.69 Å20 Å2
3---1.04 Å2
Refine analyzeLuzzati coordinate error obs: 0.221 Å
Refinement stepCycle: LAST / Resolution: 2.04→35.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3009 0 155 396 3560
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0213273
X-RAY DIFFRACTIONr_bond_other_d0.0020.022275
X-RAY DIFFRACTIONr_angle_refined_deg1.5571.9624389
X-RAY DIFFRACTIONr_angle_other_deg0.89735542
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.355401
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.5324.627134
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.68715487
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.602153
X-RAY DIFFRACTIONr_chiral_restr0.0940.2455
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213538
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02629
X-RAY DIFFRACTIONr_mcbond_it2.6731951
X-RAY DIFFRACTIONr_mcbond_other1.553802
X-RAY DIFFRACTIONr_mcangle_it4.33353151
X-RAY DIFFRACTIONr_scbond_it6.65381322
X-RAY DIFFRACTIONr_scangle_it8.476111229
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDNumberTypeRms dev position (Å)Weight position
A623medium positional0.140.5
C623medium positional0.170.5
B623medium positional0.190.5
A920loose positional0.345
C920loose positional0.335
B920loose positional0.325
A623medium thermal1.392
C623medium thermal2.192
B623medium thermal1.762
A920loose thermal1.5210
C920loose thermal2.3410
B920loose thermal1.6210
LS refinement shellResolution: 2.04→2.093 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 147 -
Rwork0.318 3179 -
obs--94.01 %
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)
13.9754-0.3251.4420.7877-1.13295.40590.081-0.176-0.0126-0.0334-0.10850.14270.02920.03340.02750.0823-0.02410.02870.0452-0.05350.0857-6.933458.621413.5763
27.05620.6068-2.52671.1725-0.96363.92620.2405-0.22690.65990.00190.07670.3185-0.32380.1565-0.31720.0756-0.01550.01820.02690.00250.1349-9.508556.00067.7572
30.5663-0.3442-0.06671.2978-0.55880.72840.0326-0.0567-0.0171-0.08440.02020.09310.04830.0057-0.05280.0864-0.00480.01340.0379-0.01590.1037-11.346947.400510.0855
43.86190.9355-2.111.43450.79056.5636-0.0208-0.1519-0.2130.1918-0.0691-0.14960.27450.24220.08990.09660.052-0.01280.06680.02870.05525.54979.240416.0243
50.08330.08790.25090.64990.14081.06650.02770.01390.04070.0144-0.0372-0.05520.02970.04740.00950.07970.04260.01470.0907-0.00060.11395.955418.92979.6673
62.4278-1.5698-0.81182.28380.63910.70010.0448-0.19460.20190.07730.0598-0.087-0.06550.0883-0.10460.09950.0110.00640.0632-0.01220.07134.790427.054915.7195
74.08141.88071.88124.29482.61124.8479-0.20430.27640.0248-0.04420.1027-0.0059-0.09190.20.10160.0739-0.05330.02790.068500.043910.607664.638913.5314
88.03884.7702-0.42173.083-0.09654.26540.03790.45210.03510.01750.2758-0.0045-0.0856-0.0259-0.31370.0167-0.00690.03080.0617-0.03370.077614.263161.215519.4641
90.746-0.7964-1.11262.66851.30751.9445-0.01630.0541-0.1373-0.01970.052-0.021-0.04310.1642-0.03570.01-0.0470.03920.2231-0.19650.227921.214756.424316.1735
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 240
2X-RAY DIFFRACTION2A241 - 275
3X-RAY DIFFRACTION3A276 - 342
4X-RAY DIFFRACTION4B-1 - 255
5X-RAY DIFFRACTION5B256 - 313
6X-RAY DIFFRACTION6B314 - 342
7X-RAY DIFFRACTION7C0 - 240
8X-RAY DIFFRACTION8C241 - 278
9X-RAY DIFFRACTION9C279 - 342

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