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- PDB-2xu7: Structural basis for RbAp48 binding to FOG-1 -

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Basic information

Entry
Database: PDB / ID: 2xu7
TitleStructural basis for RbAp48 binding to FOG-1
Components
  • HISTONE-BINDING PROTEIN RBBP4
  • ZINC FINGER PROTEIN ZFPM1
KeywordsTRANSCRIPTION / CHROMATIN REMODELLING / HISTONE CHAPERONE / COREPRESSOR / GATA1-MEDIATED REPRESSION / NURD COMPLEX
Function / homology
Function and homology information


T-helper cell lineage commitment / tricuspid valve formation / negative regulation of mast cell differentiation / regulation of definitive erythrocyte differentiation / regulation of chemokine production / definitive erythrocyte differentiation / negative regulation of interleukin-4 production / mitral valve formation / atrial septum morphogenesis / primitive erythrocyte differentiation ...T-helper cell lineage commitment / tricuspid valve formation / negative regulation of mast cell differentiation / regulation of definitive erythrocyte differentiation / regulation of chemokine production / definitive erythrocyte differentiation / negative regulation of interleukin-4 production / mitral valve formation / atrial septum morphogenesis / primitive erythrocyte differentiation / megakaryocyte differentiation / CAF-1 complex / granulocyte differentiation / NURF complex / NuRD complex / regulation of cell fate specification / negative regulation of stem cell population maintenance / DNA replication-dependent chromatin assembly / ESC/E(Z) complex / cardiac muscle tissue morphogenesis / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / regulation of stem cell differentiation / Transcription of E2F targets under negative control by DREAM complex / Polo-like kinase mediated events / atrioventricular valve morphogenesis / embryonic hemopoiesis / platelet formation / megakaryocyte development / ventricular septum morphogenesis / G1/S-Specific Transcription / positive regulation of stem cell population maintenance / ATPase complex / Sin3-type complex / Transcriptional Regulation by E2F6 / outflow tract morphogenesis / RNA Polymerase I Transcription Initiation / histone deacetylase complex / G0 and Early G1 / Cyclin E associated events during G1/S transition / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / Cyclin A:Cdk2-associated events at S phase entry / Deposition of new CENPA-containing nucleosomes at the centromere / Regulation of TP53 Activity through Acetylation / transcription repressor complex / erythrocyte differentiation / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / negative regulation of cell migration / PRC2 methylates histones and DNA / negative regulation of protein binding / Regulation of endogenous retroelements by KRAB-ZFP proteins / Regulation of PTEN gene transcription / Defective pyroptosis / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / HDACs deacetylate histones / negative regulation of transforming growth factor beta receptor signaling pathway / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / brain development / PKMTs methylate histone lysines / histone deacetylase binding / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / positive regulation of type II interferon production / transcription corepressor activity / nucleosome assembly / heart development / Factors involved in megakaryocyte development and platelet production / histone binding / Oxidative Stress Induced Senescence / RNA polymerase II-specific DNA-binding transcription factor binding / transcription regulator complex / Potential therapeutics for SARS / DNA replication / chromosome, telomeric region / chromatin remodeling / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of cell population proliferation / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / chromatin / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / nucleoplasm / nucleus / metal ion binding / cytosol
Similarity search - Function
: / Zinc finger protein ZFPM1-like, PR domain / Zinc finger CCHC FOG-type / FOG family / Zinc finger CCHC FOG-type profile. / Histone-binding protein RBBP4, N-terminal / Histone-binding protein RBBP4 or subunit C of CAF1 complex / : / Zinc-finger of C2H2 type / Zinc finger, C2H2 type ...: / Zinc finger protein ZFPM1-like, PR domain / Zinc finger CCHC FOG-type / FOG family / Zinc finger CCHC FOG-type profile. / Histone-binding protein RBBP4, N-terminal / Histone-binding protein RBBP4 or subunit C of CAF1 complex / : / Zinc-finger of C2H2 type / Zinc finger, C2H2 type / YVTN repeat-like/Quinoprotein amine dehydrogenase / zinc finger / 7 Propeller / Methylamine Dehydrogenase; Chain H / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Mainly Beta
Similarity search - Domain/homology
Histone-binding protein RBBP4 / Zinc finger protein ZFPM1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsLejon, S. / Thong, S.Y. / Murthy, A. / Blobel, G.A. / Mackay, J.P. / Murzina, N.V. / Laue, E.D.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Insights Into Association of the Nurd Complex with Fog-1 from the Crystal Structure of an Rbap48-Fog- 1 Complex.
Authors: Lejon, S. / Thong, S.Y. / Murthy, A. / Alqarni, S. / Murzina, N.V. / Blobel, G.A. / Laue, E.D. / Mackay, J.P.
History
DepositionOct 15, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 3, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: HISTONE-BINDING PROTEIN RBBP4
B: HISTONE-BINDING PROTEIN RBBP4
C: ZINC FINGER PROTEIN ZFPM1
D: ZINC FINGER PROTEIN ZFPM1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,5646
Polymers99,1754
Non-polymers3882
Water4,053225
1
A: HISTONE-BINDING PROTEIN RBBP4
D: ZINC FINGER PROTEIN ZFPM1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,7823
Polymers49,5882
Non-polymers1941
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1770 Å2
ΔGint0.3 kcal/mol
Surface area19120 Å2
MethodPISA
2
B: HISTONE-BINDING PROTEIN RBBP4
C: ZINC FINGER PROTEIN ZFPM1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,7823
Polymers49,5882
Non-polymers1941
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1670 Å2
ΔGint0.8 kcal/mol
Surface area19200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.745, 59.843, 100.648
Angle α, β, γ (deg.)90.00, 93.55, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.9374, -0.06043, 0.5353), (-0.07038, 0.996, 0.1227), (-0.3061, 0.02451, -0.8878)
Vector: -0.4781, -0.4467, -0.5079)

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Components

#1: Protein HISTONE-BINDING PROTEIN RBBP4 / CHROMATIN ASSEMBLY FACTOR 1 SUBUNIT C / CAF-1 SUBUNIT C / NUCLEOSOME-REMODELING FACTOR SUBUNIT ...CHROMATIN ASSEMBLY FACTOR 1 SUBUNIT C / CAF-1 SUBUNIT C / NUCLEOSOME-REMODELING FACTOR SUBUNIT RBAP48 / CAF-I 48 KDA SUBUNIT / CAF-I P48 / RETINOBLASTOMA-BINDING PROTEIN 4 / RBBP-4 / RETINOBLASTOMA-BINDING PROTEIN P48


Mass: 47709.527 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PFBDM / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: Q09028
#2: Protein/peptide ZINC FINGER PROTEIN ZFPM1 / FRIEND OF GATA PROTEIN 1 / FOG-1 / FRIEND OF GATA 1 / ZINC FINGER PROTEIN MULTITYPE 1


Mass: 1878.212 Da / Num. of mol.: 2 / Fragment: RBAP48-BINDING FRAGMENT, RESIDUES 1-15 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: Q8IX07
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 225 / 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: 2.3 Å3/Da / Density % sol: 46.5 % / Description: NONE
Crystal growpH: 7 / Details: 20% (W/V) PEG 3350, 0.2 M NA-MALONATE PH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763
DetectorType: ADSC CCD / Detector: CCD / Date: Jun 29, 2009 / Details: KIRKPATRICK BAEZ BIMORPH MIRROR PAIR
RadiationMonochromator: DOUBLE CRYSTAL SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.9→75.59 Å / Num. obs: 70736 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 3.2 % / Biso Wilson estimate: 19.8 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 11.3
Reflection shellResolution: 1.9→2 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 3.1 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.5.0072refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3GFC

3gfc


Resolution: 1.9→100.5 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.933 / SU B: 7.252 / SU ML: 0.099 / Cross valid method: THROUGHOUT / ESU R: 0.135 / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS.
RfactorNum. reflection% reflectionSelection details
Rfree0.22496 3576 5.1 %RANDOM
Rwork0.18315 ---
obs0.18527 67143 99.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.513 Å2
Baniso -1Baniso -2Baniso -3
1-0.95 Å20 Å2-1.25 Å2
2---1.35 Å20 Å2
3---0.24 Å2
Refinement stepCycle: LAST / Resolution: 1.9→100.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5922 0 25 225 6172
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0216104
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.861.9288314
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1835743
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.06824.821280
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.83715972
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9031523
X-RAY DIFFRACTIONr_chiral_restr0.1470.2921
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0214638
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.031.53761
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.61226100
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.7932343
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.9774.52214
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 280 -
Rwork0.254 4936 -
obs--99.79 %
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)
13.52411.43381.01621.74930.61531.86610.1176-0.3208-0.00640.3405-0.17820.2820.2103-0.43360.06060.1971-0.07640.04360.1165-0.00690.1334-43.057-9.5-22.723
21.619-0.0897-0.15942.20931.00131.67610.0892-0.2193-0.01280.3957-0.0408-0.00230.11280.0035-0.04850.1899-0.0273-0.05860.03480.02030.1052-23.708-7.235-22.813
32.6364-0.52571.60842.5444-0.39692.65040.06460.1697-0.1070.04180.0425-0.15850.15560.2598-0.10710.09540.0137-0.04740.0286-0.01380.0822-19.282-8.657-40.752
41.5736-0.9174-0.2494.29391.04571.29180.05230.14640.045-0.0981-0.07320.0605-0.0165-0.12720.02090.0968-0.0022-0.04190.0250.00650.0528-36.386-8.36-47.61
51.92461.01580.51783.6562.00843.4820.0677-0.016-0.0194-0.1941-0.11810.38920.0063-0.22870.05040.1379-0.0198-0.01880.0188-0.00840.096-44.91-12.677-41.129
617.69619.3994-2.55855.6264-4.473316.3310.0639-0.46170.00830.04760.15550.15440.3354-2.6078-0.21940.3518-0.21110.12150.75-0.29050.7277-57.71-12.301-50.594
72.49050.43130.82452.28351.52252.82140.0992-0.23670.10030.0973-0.1350.16740.0871-0.21290.03580.0985-0.0379-0.00220.0372-0.00250.0905-44.986-10.1-32.495
89.43554.6324.109513.03697.18111.70170.0460.0043-0.4009-0.079-0.17260.24340.3978-0.48430.12670.0785-0.04320.04490.07530.01990.138-50.902-17.069-31.991
93.53211.3159-0.680912.73060.22963.3895-0.11080.15740.3055-0.58820.0652-0.6411-0.24340.34770.04550.1659-0.00220.09910.1864-0.01320.253111.30824.761-28.456
101.7282-0.5198-0.02724.56141.02750.3382-0.10240.249-0.0473-0.30740.08080.0446-0.02210.05740.02160.2271-0.0165-0.06170.04920.00660.0702-10.11917.201-28.517
112.83280.0747-0.50344.72840.26711.4712-0.11650.2705-0.052-0.72190.0255-0.14350.1269-0.0770.0910.3308-0.0212-0.06980.0275-0.00090.0896-13.84815.233-25.533
123.48312.5991.4025.93091.49148.1968-0.30270.22360.4855-0.5360.22750.4189-0.4702-0.57730.07520.2062-0.0022-0.11040.07650.03740.1771-25.11820.263-21.921
133.15071.67130.86242.75460.47661.27210.1148-0.34510.1580.3836-0.17360.19850.0632-0.22670.05880.2153-0.011-0.02620.0559-0.02650.0772-16.13718.905-2.975
141.20051.6223-0.47516.7824-2.18553.45480.058-0.1073-0.03960.3819-0.0413-0.238-0.09170.0992-0.01670.17260.0172-0.11740.0164-0.01340.11331.52317.316-3.595
151.88170.35230.63383.97-0.69082.60990.01480.0897-0.08270.0535-0.0477-0.44730.06790.24350.03290.13420.0185-0.0340.0244-0.00080.14014.19217.14-17.318
1611.3525-3.18342.370910.5217-3.11167.02090.1671-0.203-0.622-0.3513-0.0515-0.52210.63070.533-0.11560.22030.01160.06220.0655-0.02030.18238.31311.568-23.838
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A16 - 114
2X-RAY DIFFRACTION2A115 - 185
3X-RAY DIFFRACTION3A186 - 267
4X-RAY DIFFRACTION4A268 - 325
5X-RAY DIFFRACTION5A326 - 350
6X-RAY DIFFRACTION6A351 - 362
7X-RAY DIFFRACTION7A363 - 398
8X-RAY DIFFRACTION8A399 - 410
9X-RAY DIFFRACTION9B12 - 36
10X-RAY DIFFRACTION10B37 - 80
11X-RAY DIFFRACTION11B81 - 138
12X-RAY DIFFRACTION12B139 - 174
13X-RAY DIFFRACTION13B175 - 279
14X-RAY DIFFRACTION14B280 - 325
15X-RAY DIFFRACTION15B326 - 398
16X-RAY DIFFRACTION16B399 - 410

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