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- PDB-6g8r: SP140 PHD-Bromodomain complex with scFv -

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Basic information

Entry
Database: PDB / ID: 6g8r
TitleSP140 PHD-Bromodomain complex with scFv
Components
  • Nuclear body protein SP140
  • single-chain variable fragment
KeywordsPEPTIDE BINDING PROTEIN / Epigenetics PHD Bromodomain Short-chain variable fragment / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


PML body / fibrillar center / defense response / DNA-binding transcription factor activity, RNA polymerase II-specific / regulation of transcription by RNA polymerase II / mitochondrion / DNA binding / nucleus / metal ion binding
Similarity search - Function
Nuclear body protein Sp140 / HSR domain / Nuclear body protein Sp110/Sp140/Sp140L / HSR domain / HSR domain profile. / SAND domain / SAND domain / SAND domain profile. / SAND domain / SAND-like domain superfamily ...Nuclear body protein Sp140 / HSR domain / Nuclear body protein Sp110/Sp140/Sp140L / HSR domain / HSR domain profile. / SAND domain / SAND domain / SAND domain profile. / SAND domain / SAND-like domain superfamily / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Zinc finger, PHD-type, conserved site / PHD-finger / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Bromodomain-like / Histone Acetyltransferase; Chain A / Zinc finger, FYVE/PHD-type / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type / Immunoglobulins / Up-down Bundle / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Nuclear body protein SP140
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.74 Å
AuthorsFairhead, M. / Graslund, S. / Strain-Damerell, C. / Picaud, S.S. / Pike, A.C.W. / Pinkas, D.M. / Wigren, E. / Preger, C. / Persson Lotsholm, H. / Ossipova, E. ...Fairhead, M. / Graslund, S. / Strain-Damerell, C. / Picaud, S.S. / Pike, A.C.W. / Pinkas, D.M. / Wigren, E. / Preger, C. / Persson Lotsholm, H. / Ossipova, E. / Filippakopoulos, P. / Burgess-Brown, N.A. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / von Delft, F. / Structural Genomics Consortium (SGC)
CitationJournal: To Be Published
Title: SP140 PHD-Bromodomain complex with scFv
Authors: Fairhead, M. / Graslund, S. / Strain-Damerell, C. / Picaud, S.S. / Pike, A.C.W. / Pinkas, D.M. / Wigren, E. / Preger, C. / Persson Lotsholm, H. / Ossipova, E. / Filippakopoulos, P. / Burgess- ...Authors: Fairhead, M. / Graslund, S. / Strain-Damerell, C. / Picaud, S.S. / Pike, A.C.W. / Pinkas, D.M. / Wigren, E. / Preger, C. / Persson Lotsholm, H. / Ossipova, E. / Filippakopoulos, P. / Burgess-Brown, N.A. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / von Delft, F.
History
DepositionApr 9, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 18, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 16, 2019Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_entity_nonpoly / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _chem_comp.name / _entity.pdbx_description ..._chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details
Revision 2.0Nov 13, 2019Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Derived calculations / Other / Refinement description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / atom_sites / computing / diffrn / entity / pdbx_distant_solvent_atoms / pdbx_entity_instance_feature / pdbx_entry_details / pdbx_nonpoly_scheme / pdbx_refine_tls / pdbx_refine_tls_group / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / pdbx_struct_oper_list / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_symm_contact / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / reflns / reflns_shell / software / struct_conf / struct_conn / struct_mon_prot_cis / struct_sheet_range / struct_site / struct_site_gen
Item: _atom_sites.fract_transf_matrix[2][1] / _atom_sites.fract_transf_matrix[3][2] ..._atom_sites.fract_transf_matrix[2][1] / _atom_sites.fract_transf_matrix[3][2] / _diffrn.pdbx_serial_crystal_experiment / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _pdbx_distant_solvent_atoms.auth_seq_id / _pdbx_distant_solvent_atoms.neighbor_macromolecule_distance / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_conn_angle.value / _pdbx_struct_sheet_hbond.range_1_auth_comp_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_comp_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_comp_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _refine.B_iso_max / _refine.B_iso_mean / _refine.B_iso_min / _refine.aniso_B[1][1] / _refine.aniso_B[1][2] / _refine.aniso_B[1][3] / _refine.aniso_B[2][2] / _refine.aniso_B[2][3] / _refine.aniso_B[3][3] / _refine.correlation_coeff_Fo_to_Fc / _refine.correlation_coeff_Fo_to_Fc_free / _refine.details / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_d_res_low / _refine.ls_number_reflns_R_free / _refine.ls_number_reflns_obs / _refine.ls_percent_reflns_R_free / _refine.ls_percent_reflns_obs / _refine.ls_wR_factor_R_free / _refine.ls_wR_factor_R_work / _refine.overall_FOM_work_R_set / _refine.overall_SU_B / _refine.overall_SU_ML / _refine.overall_SU_R_Cruickshank_DPI / _refine.overall_SU_R_free / _refine.pdbx_R_Free_selection_details / _refine.pdbx_ls_cross_valid_method / _refine.pdbx_ls_sigma_F / _refine.pdbx_overall_ESU_R / _refine.pdbx_overall_ESU_R_Free / _refine.pdbx_overall_phase_error / _refine.pdbx_solvent_ion_probe_radii / _refine.pdbx_solvent_vdw_probe_radii / _refine.pdbx_stereochemistry_target_values / _refine.solvent_model_details / _refine_hist.cycle_id / _refine_hist.d_res_low / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_B_iso_mean_ligand / _refine_hist.pdbx_B_iso_mean_solvent / _refine_hist.pdbx_number_atoms_protein / _refine_hist.pdbx_number_residues_total / _reflns.B_iso_Wilson_estimate / _reflns.d_resolution_low / _reflns.number_obs / _reflns.pdbx_CC_half / _reflns.pdbx_Rmerge_I_obs / _reflns.pdbx_Rpim_I_all / _reflns.pdbx_Rrim_I_all / _reflns.pdbx_chi_squared / _reflns.pdbx_netI_over_sigmaI / _reflns.pdbx_number_measured_all / _reflns.pdbx_redundancy / _reflns.pdbx_scaling_rejects / _reflns.percent_possible_obs / _software.name / _software.version / _struct_conn.pdbx_dist_value / _struct_sheet_range.beg_auth_comp_id / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.beg_label_comp_id / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_auth_comp_id / _struct_sheet_range.end_auth_seq_id / _struct_sheet_range.end_label_comp_id / _struct_sheet_range.end_label_seq_id / _struct_site.pdbx_num_residues
Description: Model completeness
Details: I have redefined the ASU to match the biological assembly upon request from collaborators and a publication referee, the deposited structure factors file have not been modified only the co-ordinates.
Provider: author / Type: Coordinate replacement
Revision 2.1Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: single-chain variable fragment
B: Nuclear body protein SP140
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,3586
Polymers50,1032
Non-polymers2554
Water23413
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2120 Å2
ΔGint2 kcal/mol
Surface area18380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.200, 89.200, 343.350
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

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Components

#1: Antibody single-chain variable fragment


Mass: 26590.312 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: missing density for linker region / Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#2: Protein Nuclear body protein SP140 / Lymphoid-restricted homolog of Sp100 / LYSp100 / Nuclear autoantigen Sp-140 / Speckled 140 kDa


Mass: 23512.799 Da / Num. of mol.: 1 / Fragment: UNP residues 687-862
Source method: isolated from a genetically manipulated source
Details: Zinc atoms numbered 1000 and 1001 / Source: (gene. exp.) Homo sapiens (human) / Gene: SP140, LYSP100 / Production host: Escherichia coli (E. coli) / References: UniProt: Q13342
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.94 Å3/Da / Density % sol: 68.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1.2 M sodium malonate, 0.5 % jeffamine ED-2003, 0.1 M HEPES pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96861 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96861 Å / Relative weight: 1
ReflectionResolution: 2.74→64.11 Å / Num. obs: 22312 / % possible obs: 99.5 % / Redundancy: 10.531 % / Biso Wilson estimate: 69.035 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.225 / Rrim(I) all: 0.237 / Χ2: 0.917 / Net I/σ(I): 8.93 / Num. measured all: 422035 / Scaling rejects: 98
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.74-2.8110.5943.230.7231601299229830.4423.39499.7
2.81-2.8910.5962.7340.8730358289728650.4992.87298.9
2.89-2.9710.5852.1181.1629565282027930.6312.22699
2.97-3.0610.591.5851.6629038275227420.7421.66699.6
3.06-3.1610.5821.2962.0427735263326210.7541.36199.5
3.16-3.2810.4930.922.7926863257325600.8870.96799.5
3.28-3.410.3680.6653.7525443246024540.9380.799.8
3.4-3.5410.2140.455.4224300240123790.9540.47499.1
3.54-3.6910.3290.3257.2423478229222730.9810.34299.2
3.69-3.8810.7050.2548.9923391219621850.990.26799.5
3.88-4.0810.7480.19811.6122140206520600.9910.20899.8
4.08-4.3310.6940.15713.8220725194719380.9950.16599.5
4.33-4.6310.6320.12117.0319755186018580.9970.12799.9
4.63-510.6890.10619.1718460172917270.9980.11199.9
5-5.4810.6160.1071916635157615670.9970.11299.4
5.48-6.1310.6960.11218.9315295143214300.9970.11799.9
6.13-7.0710.4380.11118.8513215126612660.9970.116100
7.07-8.6610.3310.07225.911116107610760.9990.075100
8.66-12.259.8960.04338.2381948308280.9990.04699.8
12.25-64.1110.0380.03740.4647284804710.9990.03998.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2MD8, 5FBO, 5GS3

2md8

5fbo

5gs3


Resolution: 2.74→64.11 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.931 / WRfactor Rfree: 0.22 / WRfactor Rwork: 0.1828 / FOM work R set: 0.7358 / SU B: 27.812 / SU ML: 0.234 / SU R Cruickshank DPI: 0.3535 / SU Rfree: 0.2651 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.353 / ESU R Free: 0.265 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2492 1140 5.1 %RANDOM
Rwork0.2152 ---
obs0.2169 21107 99.54 %-
Solvent computationIon probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso max: 121.97 Å2 / Biso mean: 77.703 Å2 / Biso min: 44.09 Å2
Baniso -1Baniso -2Baniso -3
1-0.55 Å20.27 Å20 Å2
2--0.55 Å20 Å2
3----1.78 Å2
Refinement stepCycle: final / Resolution: 2.74→64.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3040 0 10 13 3063
Biso mean--84.29 60.14 -
Num. residues----391
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0133124
X-RAY DIFFRACTIONr_bond_other_d0.0010.0182759
X-RAY DIFFRACTIONr_angle_refined_deg1.3011.6494212
X-RAY DIFFRACTIONr_angle_other_deg1.1281.5736391
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5555385
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.9421.635159
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.89315507
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0221520
X-RAY DIFFRACTIONr_chiral_restr0.0430.2396
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023501
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02707
LS refinement shellResolution: 2.74→2.811 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.391 84 -
Rwork0.398 1522 -
all-1606 -
obs--99.5 %
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)
11.5401-0.31150.9062.6171-0.09750.9711-0.04820.12360.0465-0.01480.0141-0.0826-0.06370.13530.0340.1808-0.04670.01710.1376-0.00790.0062-44.041743.215-5.2119
21.5959-0.45230.31713.0882-0.55061.8833-0.0068-0.0221-0.1416-0.0335-0.01390.0960.1231-0.07670.02070.1658-0.00730.02280.1322-0.01360.019-24.240828.560117.6872
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 242
2X-RAY DIFFRACTION2B686 - 862

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