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- PDB-8ye8: Crystal structure of mouse BAHCC1 TTD domain in complex with H4K2... -

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Basic information

Entry
Database: PDB / ID: 8ye8
TitleCrystal structure of mouse BAHCC1 TTD domain in complex with H4K20me1 peptide
Components
  • BAH and coiled-coil domain-containing protein 1
  • Histone H4
KeywordsPROTEIN BINDING / Bahcc1 / H4K20me
Function / homology
Function and homology information


negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Deposition of new CENPA-containing nucleosomes at the centromere ...negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Deposition of new CENPA-containing nucleosomes at the centromere / telomere organization / Inhibition of DNA recombination at telomere / Meiotic synapsis / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / SUMOylation of chromatin organization proteins / DNA methylation / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / SIRT1 negatively regulates rRNA expression / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / HDACs deacetylate histones / locomotory behavior / Nonhomologous End-Joining (NHEJ) / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / HDMs demethylate histones / G2/M DNA damage checkpoint / NoRC negatively regulates rRNA expression / DNA Damage/Telomere Stress Induced Senescence / B-WICH complex positively regulates rRNA expression / PKMTs methylate histone lysines / Meiotic recombination / Pre-NOTCH Transcription and Translation / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / HCMV Early Events / neuron differentiation / structural constituent of chromatin / nucleosome / nucleosome assembly / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / HATs acetylate histones / RUNX1 regulates transcription of genes involved in differentiation of HSCs / chromatin organization / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / Processing of DNA double-strand break ends / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / chromosome, telomeric region / Amyloid fiber formation / protein heterodimerization activity / chromatin binding / protein-containing complex / DNA binding / RNA binding / extracellular exosome / extracellular region / nucleoplasm / nucleus / membrane
Similarity search - Function
: / : / : / BAHCC1-like, Tudor domain / Bromo adjacent homology domain / BAH domain / Bromo adjacent homology (BAH) domain / Bromo adjacent homology (BAH) domain superfamily / BAH domain profile. / TATA box binding protein associated factor ...: / : / : / BAHCC1-like, Tudor domain / Bromo adjacent homology domain / BAH domain / Bromo adjacent homology (BAH) domain / Bromo adjacent homology (BAH) domain superfamily / BAH domain profile. / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Histone-fold
Similarity search - Domain/homology
Histone H4 / BAH and coiled-coil domain-containing protein 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.90001382876 Å
AuthorsZhang, Z.-M. / Song, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2025
Title: BAHCC1 binds H4K20me1 to facilitate the MCM complex loading and DNA replication.
Authors: Li, D. / Zhang, Z.M. / Mei, L. / Yu, Y. / Guo, Y. / Mackintosh, S.G. / Chen, J. / Allison, D.F. / Kim, A. / Storey, A.J. / Edmondson, R.D. / Byrum, S.D. / Tackett, A.J. / Cai, L. / Cook, J.G. ...Authors: Li, D. / Zhang, Z.M. / Mei, L. / Yu, Y. / Guo, Y. / Mackintosh, S.G. / Chen, J. / Allison, D.F. / Kim, A. / Storey, A.J. / Edmondson, R.D. / Byrum, S.D. / Tackett, A.J. / Cai, L. / Cook, J.G. / Song, J. / Wang, G.G.
History
DepositionFeb 22, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 16, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BAH and coiled-coil domain-containing protein 1
B: BAH and coiled-coil domain-containing protein 1
C: Histone H4


Theoretical massNumber of molelcules
Total (without water)32,9643
Polymers32,9643
Non-polymers00
Water2,846158
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.695, 65.286, 78.67
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein BAH and coiled-coil domain-containing protein 1


Mass: 15747.655 Da / Num. of mol.: 2 / Fragment: TTD domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Bahcc1, Kiaa1447 / Production host: Escherichia coli (E. coli) / References: UniProt: Q3UHR0
#2: Protein/peptide Histone H4


Mass: 1468.731 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P62805
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.39 Å3/Da / Density % sol: 48.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 100 mM MES, pH 6.5, 10 mM Li2SO4, 8% PEG20000 and 3 mM H4K20me

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 24054 / % possible obs: 99.9 % / Redundancy: 12.9 % / Biso Wilson estimate: 45.4 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 46
Reflection shellResolution: 1.9→1.95 Å / Rmerge(I) obs: 0.0688 / Num. unique obs: 1835

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Processing

Software
NameVersionClassification
PHENIX1.9_1692+SVNrefinement
HKL-2000data scaling
Cootmodel building
PHENIXphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: in-house Se-SAD model

Resolution: 1.90001382876→46.52450214 Å / SU ML: 0.202858156108 / Cross valid method: FREE R-VALUE / σ(F): 1.34757909605 / Phase error: 22.7475428628
RfactorNum. reflection% reflection
Rfree0.237741053839 1855 7.71181508273 %
Rwork0.187091465636 22199 -
obs0.191012499984 24054 99.925224327 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.6793616014 Å2
Refinement stepCycle: LAST / Resolution: 1.90001382876→46.52450214 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2003 0 0 158 2161
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007570960703652047
X-RAY DIFFRACTIONf_angle_d1.151810426682790
X-RAY DIFFRACTIONf_chiral_restr0.0481652040857324
X-RAY DIFFRACTIONf_plane_restr0.00495399701094365
X-RAY DIFFRACTIONf_dihedral_angle_d12.8556017909755
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9001-1.95140.2878839120071410.231426074491694X-RAY DIFFRACTION100
1.9514-2.00880.2261465213871400.2030185132551669X-RAY DIFFRACTION100
2.0088-2.07360.2331392086921410.1885377515081684X-RAY DIFFRACTION100
2.0736-2.14780.2237721765921400.1765048807951686X-RAY DIFFRACTION100
2.1478-2.23380.2136249561481420.1846855128241687X-RAY DIFFRACTION100
2.2338-2.33540.2352130766491410.1911317675071691X-RAY DIFFRACTION100
2.3354-2.45850.2653021418051400.2068626833661677X-RAY DIFFRACTION100
2.4585-2.61260.2920061781291420.207457960371709X-RAY DIFFRACTION100
2.6126-2.81420.2669576336361430.2014567443581699X-RAY DIFFRACTION100
2.8142-3.09740.259306371291420.1932946149841712X-RAY DIFFRACTION100
3.0974-3.54550.2632712829581450.1879789999461721X-RAY DIFFRACTION100
3.5455-4.46640.1891158562191450.1647892228351748X-RAY DIFFRACTION100
4.4664-46.50.2373685995121530.1866147310011822X-RAY DIFFRACTION99.1465863454
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)
14.17986230692-0.0601788306915-0.229193808434.246160575191.151547198462.76265894058-0.01192165882120.198766375543-0.310937681741-0.1865914893220.0281711980476-0.0825612863711-0.02651571550660.348094428662-0.009635106180920.316475957665-0.0194166482513-0.05004639617090.276433353045-0.001303327468380.28694024536524.1733555333-10.8307677665-10.0309457078
21.527653278932.260822112620.5033541101474.210791772630.9317772132760.26209540194-0.02820781738130.086744659466-0.1088271888850.01594020693730.02973848597020.1013290266420.0358015889775-0.0981007472139-0.01035132241960.250905248444-0.0265670876331-0.002556163778040.242914616689-0.04026533811420.27341956232121.8571460787-8.81383950003-10.2401432207
35.945759862520.6398085787841.110396775693.37990632222-0.1220015151262.97192726215-0.06894019525470.3400530152290.383169879627-0.1220249974160.03173178217790.404876927693-0.210272886438-0.1839328704650.03587176619080.2680642975030.007641753464590.006201359678080.275621868803-0.001506479912370.25663503850422.487787024510.2870514597-9.67720260855
42.445827343590.17893275852-3.08572399932.94841957248-1.419036932924.84237971393-0.215038522999-0.0403854633249-0.2098579275170.2634497673430.1659495963530.1003414978130.158362136982-0.1762532746650.007862030878230.258771628364-0.01205069329825.86375813541E-50.2459581144050.001248753497750.2677114015677.77655769556-26.1546562207-5.89638108878
55.20831342717-0.227897413329-1.586449170242.816610529940.9004599938435.068498114580.02305229499260.4941741347880.060214048472-0.280368879933-0.1414559746140.2868402486680.150020057708-0.8423676514610.04989244342420.2211188957450.00890042339398-0.03220464360110.3265369408110.004331381041080.2383404493928.55931860918-23.0685499559-27.4374422979
67.45498823052-0.505320280985-0.06259058162051.29864988027-1.594499644313.766223013930.16498415726-1.40016192165-0.157984310923-0.112928726518-0.04718211053340.3544943386410.283343865543-0.846103627238-0.2562107907930.3597575180540.120430985576-0.1146397804141.094985381720.07630762114550.5955864584337.457235185099.22815092528-10.2718747088
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1907 through 1942 )
2X-RAY DIFFRACTION2chain 'A' and (resid 1943 through 1977 )
3X-RAY DIFFRACTION3chain 'A' and (resid 1978 through 2040 )
4X-RAY DIFFRACTION4chain 'B' and (resid 1909 through 1976 )
5X-RAY DIFFRACTION5chain 'B' and (resid 1977 through 2040 )
6X-RAY DIFFRACTION6chain 'C' and (resid 18 through 23 )

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