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- PDB-6j2p: Crystal structure of Saccharomyces cerevisiae Spp1 in complex wit... -

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Basic information

Entry
Database: PDB / ID: 6j2p
TitleCrystal structure of Saccharomyces cerevisiae Spp1 in complex with H3K4me3
Components
  • COMPASS component SPP1
  • Histone H3
KeywordsPROTEIN BINDING / Histone modification recognition
Function / homology
Function and homology information


regulation of meiotic DNA double-strand break formation / Formation of WDR5-containing histone-modifying complexes / sexual sporulation resulting in formation of a cellular spore / cupric reductase (NADH) activity / global genome nucleotide-excision repair / RNA polymerase I upstream activating factor complex / Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Assembly of the ORC complex at the origin of replication ...regulation of meiotic DNA double-strand break formation / Formation of WDR5-containing histone-modifying complexes / sexual sporulation resulting in formation of a cellular spore / cupric reductase (NADH) activity / global genome nucleotide-excision repair / RNA polymerase I upstream activating factor complex / Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Assembly of the ORC complex at the origin of replication / Set1C/COMPASS complex / Oxidative Stress Induced Senescence / RNA Polymerase I Promoter Escape / positive regulation of transcription by RNA polymerase I / nucleolar large rRNA transcription by RNA polymerase I / Estrogen-dependent gene expression / rRNA transcription / intracellular copper ion homeostasis / : / subtelomeric heterochromatin formation / CENP-A containing nucleosome / aerobic respiration / structural constituent of chromatin / nucleosome / chromatin organization / chromosome, telomeric region / protein heterodimerization activity / chromatin binding / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / DNA binding / zinc ion binding / nucleus / cytosol
Similarity search - Function
Spp1/CFP1 / 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 / Zinc finger, FYVE/PHD-type / Histone H3 signature 1. ...Spp1/CFP1 / 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 / Zinc finger, FYVE/PHD-type / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Histone H3 / COMPASS component SPP1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288c (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.85 Å
AuthorsHe, C. / Li, F.
CitationJournal: Biochem.J. / Year: 2019
Title: Structural basis for histone H3K4me3 recognition by the N-terminal domain of the PHD finger protein Spp1.
Authors: He, C. / Liu, N. / Xie, D. / Liu, Y. / Xiao, Y. / Li, F.
History
DepositionJan 2, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 11, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 9, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: COMPASS component SPP1
B: COMPASS component SPP1
C: COMPASS component SPP1
D: COMPASS component SPP1
E: Histone H3
F: Histone H3
G: Histone H3
H: Histone H3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,04620
Polymers60,2618
Non-polymers78512
Water00
1
A: COMPASS component SPP1
E: Histone H3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2615
Polymers15,0652
Non-polymers1963
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1130 Å2
ΔGint-7 kcal/mol
Surface area7530 Å2
MethodPISA
2
B: COMPASS component SPP1
F: Histone H3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2615
Polymers15,0652
Non-polymers1963
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1080 Å2
ΔGint-3 kcal/mol
Surface area6960 Å2
MethodPISA
3
C: COMPASS component SPP1
H: Histone H3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2615
Polymers15,0652
Non-polymers1963
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area940 Å2
ΔGint-4 kcal/mol
Surface area6570 Å2
MethodPISA
4
D: COMPASS component SPP1
G: Histone H3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2615
Polymers15,0652
Non-polymers1963
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1130 Å2
ΔGint-42 kcal/mol
Surface area6700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.810, 106.170, 139.830
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
COMPASS component SPP1 / Complex proteins associated with SET1 protein SPP1 / Set1C component SPP1 / Suppressor of PRP protein 1


Mass: 14246.196 Da / Num. of mol.: 4 / Fragment: UNP residues 1-124
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: S288c / Gene: SPP1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q03012
#2: Protein/peptide
Histone H3


Mass: 818.961 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P61830
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Zn
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: 2.52 Å3/Da / Density % sol: 51.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M ammonium sulfate, 20% PEG3350, 0.1 M HEPES ph 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.987 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.85→69.915 Å / Num. all: 14530 / Num. obs: 14530 / % possible obs: 99.7 % / Redundancy: 5.3 % / Biso Wilson estimate: 69.48 Å2 / Rpim(I) all: 0.056 / Rrim(I) all: 0.132 / Rsym value: 0.119 / Net I/av σ(I): 5.4 / Net I/σ(I): 8.8 / Num. measured all: 77725
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
2.85-35.50.6891.11149720850.3240.7640.6892.199.9
3-3.195.50.4741.61094919920.2230.5260.474399.9
3.19-3.415.50.2682.71018718640.1260.2980.2684.8100
3.41-3.685.40.1664.3938817330.0780.1840.1667.699.8
3.68-4.035.40.1146862816060.0530.1270.11410.599.8
4.03-4.515.30.0926.9779214740.0430.1020.09213.599.6
4.51-5.250.0996.2649412950.0460.110.09914.399.7
5.2-6.3750.0896.7550011070.0420.0980.08914.599.7
6.37-9.015.50.05512.548448800.0250.060.05516.999.9
9.01-46.6150.04216.224464940.020.0470.04218.795

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
SCALA3.3.22data scaling
PDB_EXTRACT3.24data extraction
iMOSFLMdata reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.85→42.279 Å / SU ML: 0.49 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 30.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2878 726 5.01 %
Rwork0.2345 13777 -
obs0.2372 14503 99.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 169.47 Å2 / Biso mean: 78.3615 Å2 / Biso min: 31.24 Å2
Refinement stepCycle: final / Resolution: 2.85→42.279 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3171 0 12 0 3183
Biso mean--68.19 --
Num. residues----398
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023252
X-RAY DIFFRACTIONf_angle_d0.5744384
X-RAY DIFFRACTIONf_chiral_restr0.04441
X-RAY DIFFRACTIONf_plane_restr0.003558
X-RAY DIFFRACTIONf_dihedral_angle_d5.541909
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.85-3.070.42981340.324227172851100
3.07-3.37880.3391230.299827512874100
3.3788-3.86750.31481540.239827262880100
3.8675-4.87150.27391620.206927482910100
4.8715-42.28360.24521530.21432835298899

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