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- PDB-6km7: The structural basis for the internal interaction in RBBP5 -

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Basic information

Entry
Database: PDB / ID: 6km7
TitleThe structural basis for the internal interaction in RBBP5
Components(Retinoblastoma-binding protein ...) x 2
KeywordsPROTEIN BINDING / Histone methyltransferase / MLL1 complex / RBBP5 / histone methylation / epigenetics
Function / homology
Function and homology information


Loss of Function of KMT2D in MLL4 Complex Formation in Kabuki Syndrome / Epigenetic regulation of gene expression by MLL3 and MLL4 complexes / MLL3/4 complex / Set1C/COMPASS complex / MLL1/2 complex / Formation of WDR5-containing histone-modifying complexes / histone methyltransferase complex / MLL1 complex / transcription initiation-coupled chromatin remodeling / Deactivation of the beta-catenin transactivating complex ...Loss of Function of KMT2D in MLL4 Complex Formation in Kabuki Syndrome / Epigenetic regulation of gene expression by MLL3 and MLL4 complexes / MLL3/4 complex / Set1C/COMPASS complex / MLL1/2 complex / Formation of WDR5-containing histone-modifying complexes / histone methyltransferase complex / MLL1 complex / transcription initiation-coupled chromatin remodeling / Deactivation of the beta-catenin transactivating complex / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / PKMTs methylate histone lysines / response to estrogen / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Neddylation / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / histone binding / transcription cis-regulatory region binding / DNA damage response / nucleolus / nucleoplasm / nucleus
Similarity search - Function
Retinoblastoma-binding protein 5/Swd1 / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / WD domain, G-beta repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40/YVTN repeat-like-containing domain superfamily / Mainly Beta
Similarity search - Domain/homology
Retinoblastoma-binding protein 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.801 Å
AuthorsHan, J. / Li, T. / Chen, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31470737 China
CitationJournal: Nucleic Acids Res / Year: 2019
Title: The internal interaction in RBBP5 regulates assembly and activity of MLL1 methyltransferase complex.
Authors: Jianming Han / Tingting Li / Yanjing Li / Muchun Li / Xiaoman Wang / Chao Peng / Chen Su / Na Li / Yiwen Li / Ying Xu / Yong Chen /
Abstract: The Mixed Lineage Leukemia protein 1 (MLL1) plays an essential role in the maintenance of the histone H3 lysine 4 (H3K4) methylation status for gene expression during differentiation and development. ...The Mixed Lineage Leukemia protein 1 (MLL1) plays an essential role in the maintenance of the histone H3 lysine 4 (H3K4) methylation status for gene expression during differentiation and development. The methyltransferase activity of MLL1 is regulated by three conserved core subunits, WDR5, RBBP5 and ASH2L. Here, we determined the structure of human RBBP5 and demonstrated its role in the assembly and regulation of the MLL1 complex. We identified an internal interaction between the WD40 propeller and the C-terminal distal region in RBBP5, which assisted the maintenance of the compact conformation of the MLL1 complex. We also discovered a vertebrate-specific motif in the C-terminal distal region of RBBP5 that contributed to nucleosome recognition and methylation of nucleosomes by the MLL1 complex. Our results provide new insights into functional conservation and evolutionary plasticity of the scaffold protein RBBP5 in the regulation of KMT2-family methyltransferase complexes.
History
DepositionJul 31, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 2, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2019Group: Data collection / Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 13, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Retinoblastoma-binding protein 5
B: Retinoblastoma-binding protein 5
C: Retinoblastoma-binding protein 5
D: Retinoblastoma-binding protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,01515
Polymers85,3554
Non-polymers1,66011
Water8,629479
1
A: Retinoblastoma-binding protein 5
C: Retinoblastoma-binding protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,4786
Polymers42,6782
Non-polymers8014
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3600 Å2
ΔGint-48 kcal/mol
Surface area15480 Å2
MethodPISA
2
B: Retinoblastoma-binding protein 5
D: Retinoblastoma-binding protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5369
Polymers42,6782
Non-polymers8597
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4200 Å2
ΔGint-99 kcal/mol
Surface area15460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.571, 68.841, 72.788
Angle α, β, γ (deg.)99.240, 99.310, 113.810
Int Tables number1
Space group name H-MP1

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Components

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Retinoblastoma-binding protein ... , 2 types, 4 molecules ABCD

#1: Protein Retinoblastoma-binding protein 5 / WD40 propeller / RBBP-5 / Retinoblastoma-binding protein RBQ-3


Mass: 35182.211 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RBBP5, RBQ3 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: Q15291
#2: Protein Retinoblastoma-binding protein 5 / RBBP-5 / Retinoblastoma-binding protein RBQ-3


Mass: 7495.291 Da / Num. of mol.: 2 / Fragment: C-terminal distal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RBBP5, RBQ3 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: Q15291

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Non-polymers , 5 types, 490 molecules

#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-2PE / NONAETHYLENE GLYCOL


Mass: 414.488 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H38O10 / Comment: precipitant*YM
#5: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#6: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 479 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.81 Å3/Da / Density % sol: 56.2 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES-Na, pH 7.5, 2% w/v PEG 400, 2.0 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97855 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 16, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97855 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 86928 / % possible obs: 96.3 % / Redundancy: 6.7 % / Biso Wilson estimate: 22.26 Å2 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.035 / Rrim(I) all: 0.092 / Χ2: 1.525 / Net I/σ(I): 5.4 / Num. measured all: 583704
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.8-1.865.50.42180550.9110.1860.4620.5189.2
1.86-1.945.90.33684830.9370.1450.3670.54594.5
1.94-2.036.20.26987600.960.1160.2930.5796.5
2.03-2.136.60.2187260.9770.0880.2280.63596.9
2.13-2.277.10.17587590.9850.0710.1890.7697.4
2.27-2.4470.14688500.9870.0590.1580.91897.6
2.44-2.697.10.11388130.990.0450.1220.93697.5
2.69-3.087.20.08388570.9940.0330.0891.16798.2
3.08-3.887.20.0688600.9950.0240.0652.28197.9
3.88-507.20.06187650.9870.0250.0656.07997.2

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-3000data scaling
SHARPphasing
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
RefinementMethod to determine structure: SAD / Resolution: 1.801→34.772 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 2.23 / Phase error: 17.93
RfactorNum. reflection% reflection
Rfree0.1943 4354 5.01 %
Rwork0.1649 --
obs0.1664 86883 96.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 111.63 Å2 / Biso mean: 32.2039 Å2 / Biso min: 10.01 Å2
Refinement stepCycle: final / Resolution: 1.801→34.772 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5382 0 168 479 6029
Biso mean--59.17 41.54 -
Num. residues----682
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085587
X-RAY DIFFRACTIONf_angle_d0.9627570
X-RAY DIFFRACTIONf_chiral_restr0.068861
X-RAY DIFFRACTIONf_plane_restr0.006947
X-RAY DIFFRACTIONf_dihedral_angle_d12.9613342
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.801-1.82150.30471120.2657238384
1.8215-1.84290.28771220.2502256590
1.8429-1.86540.27251300.2341266092
1.8654-1.8890.27231530.2247262193
1.889-1.91390.22361450.1989274695
1.9139-1.94010.24051380.1955268595
1.9401-1.96780.22021480.1862283396
1.9678-1.99720.18181390.178274997
1.9972-2.02840.20361580.1746274496
2.0284-2.06160.21131350.1695275397
2.0616-2.09720.19271430.1635274697
2.0972-2.13530.21241430.168281997
2.1353-2.17630.18391390.1667278897
2.1763-2.22080.19751720.1699276697
2.2208-2.2690.17661660.1594273497
2.269-2.32180.21341640.1652281998
2.3218-2.37990.20931590.1682278998
2.3799-2.44420.22521380.1691278997
2.4442-2.51610.22061540.1696274996
2.5161-2.59730.18691690.1602279198
2.5973-2.69010.19881280.1598282798
2.6901-2.79770.19341450.1588281998
2.7977-2.9250.18721410.1626281598
2.925-3.07910.20431270.1679281198
3.0791-3.27190.1931380.1593277696
3.2719-3.52430.18461420.1515282599
3.5243-3.87860.15241610.1452283099
3.8786-4.43880.17181530.1403280198
4.4388-5.58870.16861420.1467275997
5.5887-34.7720.20961500.1882273796
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)
11.14240.12820.00311.17920.31882.40530.0224-0.02990.14430.04960.01140.0627-0.1816-0.1183-0.02330.13020.01410.01830.08360.00320.158131.242380.37223.6308
22.0716-0.6091.5450.6808-0.69023.96490.17220.2157-0.1629-0.1795-0.0946-0.05230.3330.3409-0.04770.17080.01710.00130.1822-0.02510.18947.935369.2994-6.0234
33.1595-1.4709-0.13792.4387-0.2153.1026-0.0409-0.383-0.0510.18080.083-0.18910.01210.254-0.04250.1266-0.0284-0.02830.168-0.01050.165248.344174.446513.9931
40.79340.07490.35471.2518-0.71723.229-0.0233-0.02390.05120.03870.03840.0091-0.0287-0.0648-0.01340.09180.03110.01280.1319-0.01490.14417.332160.048427.3068
51.23160.59060.18931.86731.29834.86510.0392-0.1149-0.22590.25130.0918-0.02860.7309-0.0895-0.07050.2916-0.0301-0.03250.1670.01970.192413.81339.696235.7083
60.6434-0.0961.28934.2472-0.52572.6288-0.01080.0269-0.2599-0.42430.28620.11620.5688-0.3619-0.14320.2623-0.1089-0.03810.21190.01490.201210.412944.992216.5047
79.02510.7962-2.14864.16432.57845.45950.30330.03681.04170.09380.32520.4926-1.5093-0.075-0.61940.59480.06240.03610.2166-0.010.426933.623996.58366.6916
83.7022-4.0685-4.0534.49374.47784.4830.08630.10210.63580.0656-0.04650.5758-0.4208-1.1329-0.04940.26270.0486-0.0280.49090.00010.409216.58177.5642-6.2426
91.25290.4986-0.70895.79340.96697.50910.0349-0.0184-0.3651-0.3915-0.03310.75150.9951-0.8809-0.01830.3405-0.1109-0.02530.3161-0.03340.279123.165362.8499-8.1863
102.3190.75142.02675.2936-1.49467.24370.29590.0128-0.85030.0314-0.2558-0.61390.8334-0.1549-0.03730.34770.01090.02470.26830.02120.291229.469661.34595.2832
116.89744.23833.80754.46341.18324.9736-0.43870.0540.37060.07550.50680.244-0.54890.3923-0.24290.74980.03270.03260.8162-0.02990.76019.760173.483823.6816
127.0837-4.29890.93143.4549-2.50544.611-0.06480.35960.52960.2556-0.4237-0.6677-0.46940.95550.40.2967-0.0758-0.09630.47880.00820.284732.646862.505436.6618
135.76892.15271.6432.78851.17083.48990.61090.2726-1.3332-0.4187-0.2761-0.98681.11681.5369-0.27660.45060.22520.0540.491-0.00890.471733.169850.798424.4111
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 12 through 144 )A12 - 144
2X-RAY DIFFRACTION2chain 'A' and (resid 145 through 270 )A145 - 270
3X-RAY DIFFRACTION3chain 'A' and (resid 271 through 324 )A271 - 324
4X-RAY DIFFRACTION4chain 'B' and (resid 12 through 164 )B12 - 164
5X-RAY DIFFRACTION5chain 'B' and (resid 165 through 253 )B165 - 253
6X-RAY DIFFRACTION6chain 'B' and (resid 254 through 323 )B254 - 323
7X-RAY DIFFRACTION7chain 'C' and (resid 396 through 404 )C396 - 404
8X-RAY DIFFRACTION8chain 'C' and (resid 452 through 456 )C452 - 456
9X-RAY DIFFRACTION9chain 'C' and (resid 457 through 466 )C457 - 466
10X-RAY DIFFRACTION10chain 'C' and (resid 467 through 474 )C467 - 474
11X-RAY DIFFRACTION11chain 'D' and (resid 397 through 450 )D397 - 450
12X-RAY DIFFRACTION12chain 'D' and (resid 451 through 465 )D451 - 465
13X-RAY DIFFRACTION13chain 'D' and (resid 466 through 474 )D466 - 474

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