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- PDB-6wat: complex structure of PHF1 -

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Basic information

Entry
Database: PDB / ID: 6wat
Titlecomplex structure of PHF1
Components
  • Histone H3.1t peptide
  • PHD finger protein 1
KeywordsGENE REGULATION / PHF1 / Tudor / histone variant / complex / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


histone methyltransferase binding / DNA repair-dependent chromatin remodeling / 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 / methylated histone binding / Inhibition of DNA recombination at telomere / Meiotic synapsis ...histone methyltransferase binding / DNA repair-dependent chromatin remodeling / 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 / methylated histone binding / Inhibition of DNA recombination at telomere / Meiotic synapsis / Condensation of Prophase Chromosomes / transcription corepressor binding / PRC2 methylates histones and DNA / Nonhomologous End-Joining (NHEJ) / Formation of the beta-catenin:TCF transactivating complex / G2/M DNA damage checkpoint / DNA Damage/Telomere Stress Induced Senescence / Meiotic recombination / nucleosome assembly / structural constituent of chromatin / nucleosome / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / site of double-strand break / chromatin organization / Processing of DNA double-strand break ends / chromosome, telomeric region / protein heterodimerization activity / centrosome / chromatin binding / regulation of DNA-templated transcription / DNA binding / extracellular exosome / nucleoplasm / identical protein binding / metal ion binding / nucleus / cytosol
Similarity search - Function
: / : / PHD finger protein 1 / Polycomb-like MTF2 factor 2, C-terminal domain / Polycomb-like MTF2 factor 2 / Lysine-specific demethylase 4, Tudor domain / Jumonji domain-containing protein 2A Tudor domain / Tudor domain / Tudor domain / Zinc finger, PHD-type, conserved site ...: / : / PHD finger protein 1 / Polycomb-like MTF2 factor 2, C-terminal domain / Polycomb-like MTF2 factor 2 / Lysine-specific demethylase 4, Tudor domain / Jumonji domain-containing protein 2A Tudor domain / Tudor domain / Tudor domain / Zinc finger, PHD-type, conserved site / PHD-finger / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Histone H3 signature 1. / Zinc finger, PHD-type / PHD zinc finger / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Zinc finger, FYVE/PHD-type / Histone-fold / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
PHD finger protein 1 / Histone H3.1t
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsDong, C. / Bountra, C. / Edwards, A.M. / Arrowsmith, C.H. / Min, J.R. / Structural Genomics Consortium (SGC)
CitationJournal: Elife / Year: 2020
Title: Structural basis for histone variant H3tK27me3 recognition by PHF1 and PHF19.
Authors: Dong, C. / Nakagawa, R. / Oyama, K. / Yamamoto, Y. / Zhang, W. / Dong, A. / Li, Y. / Yoshimura, Y. / Kamiya, H. / Nakayama, J.I. / Ueda, J. / Min, J.
History
DepositionMar 26, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 16, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 18, 2023Group: 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
AA: PHD finger protein 1
AC: PHD finger protein 1
BA: PHD finger protein 1
BC: PHD finger protein 1
CA: PHD finger protein 1
CC: PHD finger protein 1
DA: PHD finger protein 1
DC: PHD finger protein 1
EA: PHD finger protein 1
EC: PHD finger protein 1
FA: PHD finger protein 1
FC: PHD finger protein 1
GA: PHD finger protein 1
GC: PHD finger protein 1
HA: PHD finger protein 1
HC: PHD finger protein 1
IA: PHD finger protein 1
IC: PHD finger protein 1
JA: PHD finger protein 1
JC: PHD finger protein 1
KA: PHD finger protein 1
KC: PHD finger protein 1
LA: PHD finger protein 1
LC: PHD finger protein 1
MA: PHD finger protein 1
MC: PHD finger protein 1
NA: PHD finger protein 1
NC: PHD finger protein 1
OA: PHD finger protein 1
OC: PHD finger protein 1
A: Histone H3.1t peptide
B: Histone H3.1t peptide
C: Histone H3.1t peptide
D: Histone H3.1t peptide
E: Histone H3.1t peptide
F: Histone H3.1t peptide
G: Histone H3.1t peptide
H: Histone H3.1t peptide
I: Histone H3.1t peptide
J: Histone H3.1t peptide
K: Histone H3.1t peptide
L: Histone H3.1t peptide
M: Histone H3.1t peptide
N: Histone H3.1t peptide
O: Histone H3.1t peptide
P: Histone H3.1t peptide
Q: Histone H3.1t peptide
R: Histone H3.1t peptide
S: Histone H3.1t peptide
T: Histone H3.1t peptide
V: Histone H3.1t peptide
Y: Histone H3.1t peptide
Z: Histone H3.1t peptide
a: Histone H3.1t peptide
b: Histone H3.1t peptide
c: Histone H3.1t peptide
d: Histone H3.1t peptide
e: Histone H3.1t peptide
f: Histone H3.1t peptide
g: Histone H3.1t peptide


Theoretical massNumber of molelcules
Total (without water)238,712190
Polymers238,71260
Non-polymers0130
Water10,160564
1
AA: PHD finger protein 1
AC: PHD finger protein 1
A: Histone H3.1t peptide
B: Histone H3.1t peptide


Theoretical massNumber of molelcules
Total (without water)15,91416
Polymers15,9144
Non-polymers012
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4670 Å2
ΔGint-32 kcal/mol
Surface area7270 Å2
MethodPISA
2
BA: PHD finger protein 1
BC: PHD finger protein 1
C: Histone H3.1t peptide
D: Histone H3.1t peptide


Theoretical massNumber of molelcules
Total (without water)15,91415
Polymers15,9144
Non-polymers011
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4600 Å2
ΔGint-34 kcal/mol
Surface area7410 Å2
MethodPISA
3
CA: PHD finger protein 1
CC: PHD finger protein 1
E: Histone H3.1t peptide
F: Histone H3.1t peptide


Theoretical massNumber of molelcules
Total (without water)15,91419
Polymers15,9144
Non-polymers015
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4950 Å2
ΔGint-36 kcal/mol
Surface area7190 Å2
MethodPISA
4
DA: PHD finger protein 1
DC: PHD finger protein 1
G: Histone H3.1t peptide
H: Histone H3.1t peptide


Theoretical massNumber of molelcules
Total (without water)15,91415
Polymers15,9144
Non-polymers011
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4710 Å2
ΔGint-34 kcal/mol
Surface area7400 Å2
MethodPISA
5
EA: PHD finger protein 1
EC: PHD finger protein 1
I: Histone H3.1t peptide
J: Histone H3.1t peptide


Theoretical massNumber of molelcules
Total (without water)15,91422
Polymers15,9144
Non-polymers018
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4640 Å2
ΔGint-33 kcal/mol
Surface area7400 Å2
MethodPISA
6
FA: PHD finger protein 1
FC: PHD finger protein 1
K: Histone H3.1t peptide
L: Histone H3.1t peptide


Theoretical massNumber of molelcules
Total (without water)15,91416
Polymers15,9144
Non-polymers012
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4550 Å2
ΔGint-35 kcal/mol
Surface area7410 Å2
MethodPISA
7
GA: PHD finger protein 1
GC: PHD finger protein 1
M: Histone H3.1t peptide
N: Histone H3.1t peptide


Theoretical massNumber of molelcules
Total (without water)15,91412
Polymers15,9144
Non-polymers08
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4660 Å2
ΔGint-36 kcal/mol
Surface area7140 Å2
MethodPISA
8
HA: PHD finger protein 1
HC: PHD finger protein 1
O: Histone H3.1t peptide
P: Histone H3.1t peptide


Theoretical massNumber of molelcules
Total (without water)15,91419
Polymers15,9144
Non-polymers015
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4820 Å2
ΔGint-36 kcal/mol
Surface area7180 Å2
MethodPISA
9
IA: PHD finger protein 1
IC: PHD finger protein 1
Q: Histone H3.1t peptide
R: Histone H3.1t peptide


Theoretical massNumber of molelcules
Total (without water)15,9148
Polymers15,9144
Non-polymers04
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4360 Å2
ΔGint-35 kcal/mol
Surface area7220 Å2
MethodPISA
10
JA: PHD finger protein 1
JC: PHD finger protein 1
S: Histone H3.1t peptide
T: Histone H3.1t peptide


Theoretical massNumber of molelcules
Total (without water)15,91414
Polymers15,9144
Non-polymers010
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4580 Å2
ΔGint-33 kcal/mol
Surface area7170 Å2
MethodPISA
11
KA: PHD finger protein 1
KC: PHD finger protein 1
V: Histone H3.1t peptide
Y: Histone H3.1t peptide


Theoretical massNumber of molelcules
Total (without water)15,9146
Polymers15,9144
Non-polymers02
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4190 Å2
ΔGint-37 kcal/mol
Surface area6900 Å2
MethodPISA
12
LA: PHD finger protein 1
LC: PHD finger protein 1
Z: Histone H3.1t peptide
a: Histone H3.1t peptide


Theoretical massNumber of molelcules
Total (without water)15,9147
Polymers15,9144
Non-polymers03
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4350 Å2
ΔGint-33 kcal/mol
Surface area7200 Å2
MethodPISA
13
MA: PHD finger protein 1
MC: PHD finger protein 1
b: Histone H3.1t peptide
c: Histone H3.1t peptide


Theoretical massNumber of molelcules
Total (without water)15,9146
Polymers15,9144
Non-polymers02
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3980 Å2
ΔGint-37 kcal/mol
Surface area7040 Å2
MethodPISA
14
NA: PHD finger protein 1
NC: PHD finger protein 1
d: Histone H3.1t peptide
e: Histone H3.1t peptide


Theoretical massNumber of molelcules
Total (without water)15,9148
Polymers15,9144
Non-polymers04
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3980 Å2
ΔGint-34 kcal/mol
Surface area7080 Å2
MethodPISA
15
OA: PHD finger protein 1
OC: PHD finger protein 1
f: Histone H3.1t peptide
g: Histone H3.1t peptide


Theoretical massNumber of molelcules
Total (without water)15,9147
Polymers15,9144
Non-polymers03
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4000 Å2
ΔGint-33 kcal/mol
Surface area7040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.753, 286.814, 123.536
Angle α, β, γ (deg.)90.000, 90.720, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein ...
PHD finger protein 1 / / hPHF1 / Polycomb-like protein 1 / hPCl1


Mass: 6938.849 Da / Num. of mol.: 30
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PHF1, PCL1 / Plasmid: pET28-MHL / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): -V3R / References: UniProt: O43189
#2: Protein/peptide ...
Histone H3.1t peptide / H3t / H3/g


Mass: 1018.231 Da / Num. of mol.: 30 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q16695
#3: Chemical...
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 130 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 564 / Source method: isolated from a natural source / Formula: H2O
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: 2.43 Å3/Da / Density % sol: 49.39 % / Mosaicity: 0.14 °
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 2.4M ammonium phosphate dibasic and 0.1M HEPES pH7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97625 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Sep 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.8→47.8 Å / Num. obs: 207862 / % possible obs: 99.2 % / Redundancy: 3.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.042 / Rrim(I) all: 0.082 / Net I/σ(I): 10.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.8-1.833.30.9393207398090.7060.5981.1171.393.7
9.86-47.83.80.028494612990.9980.0180.0342298.6

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Processing

Software
NameVersionClassification
PHENIX1.17.1refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HCZ

4hcz


Resolution: 1.8→40.76 Å / SU ML: 0.2387 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 36.2578
RfactorNum. reflection% reflection
Rfree0.268 19950 5.04 %
Rwork0.2338 --
obs0.2356 206861 94.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 32.19 Å2
Refinement stepCycle: LAST / Resolution: 1.8→40.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13744 0 1983 564 16291
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005916075
X-RAY DIFFRACTIONf_angle_d0.824721993
X-RAY DIFFRACTIONf_chiral_restr0.05742536
X-RAY DIFFRACTIONf_plane_restr0.00422748
X-RAY DIFFRACTIONf_dihedral_angle_d18.65795588
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.820.41766070.381611268X-RAY DIFFRACTION83.89
1.82-1.840.39186010.369111961X-RAY DIFFRACTION92.01
1.84-1.860.37725450.343512257X-RAY DIFFRACTION93.18
1.86-1.890.34985690.329612496X-RAY DIFFRACTION93.68
1.89-1.910.35846690.323812567X-RAY DIFFRACTION93.84
1.91-1.940.3417030.302712293X-RAY DIFFRACTION93.72
1.94-1.970.32527250.293212132X-RAY DIFFRACTION93.97
1.97-20.29336370.278812401X-RAY DIFFRACTION94.1
2-2.030.28536310.265612596X-RAY DIFFRACTION94.17
2.03-2.060.31077170.257512454X-RAY DIFFRACTION94.15
2.06-2.10.26636440.257412240X-RAY DIFFRACTION94.27
2.1-2.130.27816340.24912490X-RAY DIFFRACTION94.43
2.13-2.180.2767560.240512624X-RAY DIFFRACTION94.59
2.18-2.220.28487000.2412229X-RAY DIFFRACTION94.67
2.22-2.270.26816130.238812578X-RAY DIFFRACTION95.29
2.27-2.320.28967520.236712644X-RAY DIFFRACTION95.34
2.32-2.380.29426730.255612531X-RAY DIFFRACTION95.28
2.38-2.440.28676830.2512455X-RAY DIFFRACTION95.68
2.44-2.510.3056970.261412990X-RAY DIFFRACTION95.9
2.51-2.60.32556450.253912354X-RAY DIFFRACTION95.83
2.6-2.690.31927330.26212706X-RAY DIFFRACTION96.26
2.69-2.80.31077300.247812630X-RAY DIFFRACTION96.36
2.8-2.920.27296540.237712817X-RAY DIFFRACTION96.83
2.92-3.080.27136360.232912775X-RAY DIFFRACTION96.99
3.08-3.270.27397060.232913068X-RAY DIFFRACTION97.37
3.27-3.520.24666500.210212712X-RAY DIFFRACTION97.84
3.52-3.880.22146620.200212990X-RAY DIFFRACTION98.35
3.88-4.440.1866050.16413094X-RAY DIFFRACTION98.65
4.44-5.590.19557030.178413159X-RAY DIFFRACTION99.08
5.59-40.760.25566700.223412005X-RAY DIFFRACTION91.52

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