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- PDB-7lky: Crystal Structure of PHF1 Tudor domain in complex with a peptidom... -

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Basic information

Entry
Database: PDB / ID: 7lky
TitleCrystal Structure of PHF1 Tudor domain in complex with a peptidomimetic ligand UNC6641
Components
  • Isoform 1 of PHD finger protein 1
  • Peptidomimetic inhibitor UNC6641
KeywordsTranscription/Transcription Inhibitor / Epigenetic reader / peptidomimetic inhibitor / Transcription-Transcription Inhibitor complex
Function / homology
Function and homology information


histone H3K36me3 reader activity / histone methyltransferase binding / ESC/E(Z) complex / histone H3K4me3 reader activity / DNA repair-dependent chromatin remodeling / negative regulation of gene expression, epigenetic / : / transcription corepressor binding / PRC2 methylates histones and DNA / site of double-strand break ...histone H3K36me3 reader activity / histone methyltransferase binding / ESC/E(Z) complex / histone H3K4me3 reader activity / DNA repair-dependent chromatin remodeling / negative regulation of gene expression, epigenetic / : / transcription corepressor binding / PRC2 methylates histones and DNA / site of double-strand break / centrosome / chromatin binding / DNA binding / zinc ion binding / nucleoplasm / identical protein 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 / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
PHD finger protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsLiu, J. / Kutateladze, T.G.
CitationJournal: J.Med.Chem. / Year: 2021
Title: Discovery of an H3K36me3-Derived Peptidomimetic Ligand with Enhanced Affinity for Plant Homeodomain Finger Protein 1 (PHF1).
Authors: Engelberg, I.A. / Liu, J. / Norris-Drouin, J.L. / Cholensky, S.H. / Ottavi, S.A. / Frye, S.V. / Kutateladze, T.G. / James, L.I.
History
DepositionFeb 3, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 15, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Isoform 1 of PHD finger protein 1
B: Isoform 1 of PHD finger protein 1
C: Isoform 1 of PHD finger protein 1
D: Isoform 1 of PHD finger protein 1
E: Isoform 1 of PHD finger protein 1
F: Isoform 1 of PHD finger protein 1
G: Isoform 1 of PHD finger protein 1
H: Isoform 1 of PHD finger protein 1
J: Peptidomimetic inhibitor UNC6641
I: Peptidomimetic inhibitor UNC6641
K: Peptidomimetic inhibitor UNC6641
L: Peptidomimetic inhibitor UNC6641
M: Peptidomimetic inhibitor UNC6641
N: Peptidomimetic inhibitor UNC6641
O: Peptidomimetic inhibitor UNC6641
P: Peptidomimetic inhibitor UNC6641
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,29525
Polymers65,66816
Non-polymers6279
Water4,648258
1
A: Isoform 1 of PHD finger protein 1
J: Peptidomimetic inhibitor UNC6641
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,3394
Polymers8,2082
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area430 Å2
ΔGint-28 kcal/mol
Surface area5690 Å2
MethodPISA
2
I: Peptidomimetic inhibitor UNC6641

B: Isoform 1 of PHD finger protein 1


Theoretical massNumber of molelcules
Total (without water)8,2082
Polymers8,2082
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_556x,y,z+11
Buried area310 Å2
ΔGint-25 kcal/mol
Surface area5250 Å2
MethodPISA
3
C: Isoform 1 of PHD finger protein 1
K: Peptidomimetic inhibitor UNC6641
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,2743
Polymers8,2082
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1260 Å2
ΔGint-38 kcal/mol
Surface area4210 Å2
MethodPISA
4
D: Isoform 1 of PHD finger protein 1
L: Peptidomimetic inhibitor UNC6641
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,3524
Polymers8,2082
Non-polymers1442
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1190 Å2
ΔGint-42 kcal/mol
Surface area4360 Å2
MethodPISA
5
E: Isoform 1 of PHD finger protein 1
M: Peptidomimetic inhibitor UNC6641
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,3524
Polymers8,2082
Non-polymers1442
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1360 Å2
ΔGint-33 kcal/mol
Surface area4530 Å2
MethodPISA
6
F: Isoform 1 of PHD finger protein 1
N: Peptidomimetic inhibitor UNC6641


Theoretical massNumber of molelcules
Total (without water)8,2082
Polymers8,2082
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1080 Å2
ΔGint-5 kcal/mol
Surface area4360 Å2
MethodPISA
7
G: Isoform 1 of PHD finger protein 1
O: Peptidomimetic inhibitor UNC6641
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,2873
Polymers8,2082
Non-polymers781
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1100 Å2
ΔGint-4 kcal/mol
Surface area4390 Å2
MethodPISA
8
H: Isoform 1 of PHD finger protein 1
P: Peptidomimetic inhibitor UNC6641
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,2743
Polymers8,2082
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1300 Å2
ΔGint-30 kcal/mol
Surface area4590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.394, 45.345, 64.442
Angle α, β, γ (deg.)90.020, 95.190, 90.070
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 7206.173 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Details: Chemical modification on the side chain of Lysine 4 of the peptidomimetic inhibitor
Source: (gene. exp.) Homo sapiens (human) / Gene: PHF1, PCL1 / Production host: Escherichia coli (E. coli) / References: UniProt: O43189
#2: Protein/peptide
Peptidomimetic inhibitor UNC6641


Mass: 1002.297 Da / Num. of mol.: 8 / Source method: obtained synthetically
Details: Chemical modification on the side chain of Lysine 4 of the peptidomimetic inhibitor
Source: (synth.) synthetic construct (others)
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 258 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.96 Å3/Da / Density % sol: 37.17 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion / Details: 0.01 M ZnCl2, 0.1 M MES pH 6.0 and 20% PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.28 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Aug 17, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28 Å / Relative weight: 1
Reflection twinOperator: -h,k,-l / Fraction: 0.48
ReflectionResolution: 1.85→43.22 Å / Num. obs: 37960 / % possible obs: 90.87 % / Redundancy: 1.9 % / CC1/2: 0.997 / CC star: 0.999 / Net I/σ(I): 8.85
Reflection shellResolution: 1.85→1.92 Å / Rmerge(I) obs: 0.3336 / Num. unique obs: 2652

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.25data extraction
autoXDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HCZ

4hcz


Resolution: 1.85→43.22 Å / Cross valid method: THROUGHOUT / σ(F): 1.75 / Phase error: 31.24 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.281 2052 5.41 %
Rwork0.2327 36025 -
obs0.2372 37960 90.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 79.66 Å2 / Biso mean: 19.9801 Å2 / Biso min: 5.2 Å2
Refinement stepCycle: final / Resolution: 1.85→43.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3982 0 137 258 4377
Biso mean--20.07 17.56 -
Num. residues----501
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.85-1.90.4001910.27191741183258
1.9-1.950.29431070.25022028213570
1.95-20.28231450.24372594273987
2-2.070.31751430.24342768291191
2.07-2.140.28271480.23872675282391
2.14-2.230.30391490.2412701285091
2.23-2.330.29561500.2382733288391
2.33-2.450.34011440.25632714285891
2.45-2.610.27381440.27082678282290
2.61-2.810.27881540.25742730288491
2.81-3.090.27531400.23912689282990
3.09-3.540.28011410.21182645278689
3.54-4.450.24871390.19272671281090
4.46-43.220.27861400.24572658279889
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)
10.01720.014-0.00010.0188-0.00590.0102-0.020.0059-0.0034-0.0012-0.01770.0048-0.0038-0.0013-0.0456-0.0537-0.0274-0.00590.03820.03670.21491.21569.586324.6821
20.00290.00810.00140.01960.00290.00160.00510.0365-0.0102-0.01460.0215-0.00840.0013-0.01690.0223-0.0599-0.03310.0130.09610.03120.243.81219.275424.1712
32222-8.95992-0.17882.6291-1.6135-1.02680.47260.78011.5049-1.3815-0.2940.33940.02150.09870.2720.0310.2583-15.686118.208216.7488
40.0003-0.00010.00070.00030.00050.0031-0.00050.00140.0050.0028-0.0026-0.0021-0.007-0.00100.13260.02290.02750.14920.0310.24812.772115.9711-9.9639
50.009-0.00120.00190.0004-0.0005-0.0004-0.00670.0069-0.0133-0.0025-0.00430.0002-0.0080-0.0095-0.00660.032-0.00330.0706-0.01980.17894.66814.5012-6.118
60.005-0.0012-0.0010.0027-0.00030.00050.0240.0024-0.00860.0023-0.0073-0.0150.00040.00720.0281-0.0084-0.03180.00930.1360.00590.1939.39028.4081-5.0293
70.00190.00260.00060.00320.00070.00080.00610.0035-0.0067-0.00450.0035-0.0072-0.00220.00060.0122-0.01690.0159-0.03280.13030.02180.15343.93076.8827-10.368
80.0056-0.0001-0.00050.00010.0002-0.00010.00670.00730.004-0.0015-0.001-0.00030.0009-0.00690.00420.02570.0180.00880.12070.00540.22099.2905-10.580932.6377
90.0196-0.0007-0.0044-0.0005-0.00060.0045-0.01960.017-0.01840.01280.00290.00150.0083-0.0037-0.0174-0.1017-0.01650.04550.0454-0.02590.219713.679-14.853735.2731
100.00330.0009-0.00130.0007-0.00110.0035-0.0083-0.0114-0.00710.0025-0.0124-0.00070.00220.016-0.00690.0451-0.03820.00490.10930.01560.246426.13917.992630.0686
110.0058-0.0088-0.00110.01360.0016-0.00060.0129-0.03530.009-0.00270.0201-0.02040.0068-0.01860.031-0.0707-0.00060.02210.1172-0.00530.222822.88029.249629.0144
120.00460.0040.00280.0070.00080.00240.0068-0.00660.00120.0012-0.0067-0.0015-0.00290.01060.00070.0212-0.04350.00470.0882-0.03440.2183-5.6246-9.226941.0232
130.02330.00890.00640.00330.00170.0041-0.0143-0.00990.004-0.0033-0.0061-0.00140.0077-0.0134-0.0329-0.0597-0.0128-0.01770.0472-0.0580.1689-11.4033-14.831337.342
140.0350.0012-0.01590.00120.00190.02120.0061-0.0108-0.00270.00170.0149-0.0040.00150.01320.01190.00770.01030.02860.0226-0.03190.1812-7.6495-14.006242.3363
150.0079-0.00350.00350.0027-0.00120.0059-0.0153-0.00730.019-0.0012-0.0164-0.00940.0057-0.0095-0.02020.01060.00470.03920.0463-0.02140.177129.09045.4235-2.558
160.020.0203-0.00290.0231-0.00720.00830.0020.00330.00740.0050.01220.015-0.01370.00160.00830.0151-0.02920.03280.0801-0.02130.202226.47068.6763-4.4475
170.0039-0.0005-0.0025-00.00040.003-0.00030.00120.0021-0.00180.00030.00170.0023-0.00510.00090.00410.0025-0.01250.0851-0.01540.158522.62398.1466-4.9681
180.00410.00070.0030.00090.00080.0055-0.0087-0.0013-0.00450.0019-0.00240.0120.00810.0046-0.00930.0044-0.01320.01460.1032-0.00710.165628.15715.68410.1276
190.0028-0.0044-0.00440.01260.00770.0070.00430.00020.0001-0.0054-0.0066-0.0041-0.00030.0059-0.00140.04790.033-0.00080.1843-0.01690.231712.8382-8.4631-1.4757
200.0165-0.00420.0120.0018-0.00260.00990.0044-0.00550.00360.0029-0.0064-0.00090.0010.0116-0.0041-0.1169-0.01670.03550.04670.00010.241816.1804-16.90723.0702
210.0121-0.012-0.00720.01310.010.0105-0.003-0.0010.00450.0036-0.00250.0052-0.00090.0032-0.00240.045300.04290.14160.00080.2656-3.4389-6.448210.3039
220.0192-0.00170.01150.0004-0.00070.0186-0.00910.0179-0.004-0.0037-0.010.0075-0.0044-0.0043-0.0179-0.0460.01940.01390.117-0.02750.1972-5.3741-18.2155.7096
230.00520.00010.001-0.00060.00110.00270.0086-0.00280.0029-0.00850.00070.0090.00360.00190.0213-0.0316-0.0009-0.00180.0716-0.03630.1733-10.2591-14.32784.7326
240.0066-0.0059-0.00710.00440.00670.00640.0058-0.00090.00390.00480.01020.0115-0.00050.00340.0114-0.0159-0.01190.03010.0886-0.04130.1724-4.743-15.770810.0882
250.0009-0.00010.00060.00340.00270.00330.0036-0.00320.00210.00030.00560.007-0.0005-0.00350.00450.06440.0119-0.0060.13540.00580.18060.6842-0.1713.6548
260.0030.00140.00220.00210.00540.0147-0.0053-0.002-0.00780.005-0.00650.00240.0003-0.0028-0.00310.10790.01240.02030.12740.00470.2488-2.29981.429335.4442
270.00250.0020.00270.00260.00350.00450.0030.0016-0.00290.00420.00090.0029-0.0056-0.008300.21420.01350.07030.2095-0.03560.27927.7096-18.773146.8183
280.0033-0.00280.00320.0035-0.00460.00550.00210.0014-0.0003-0.00060.0038-0.00340.00410.00410.00010.1711-0.04660.06660.17770.02240.241329.06373.513816.9749
290.0024-0.00140.00280.001-0.00220.00590.0038-0.0015-0.0006-0.0046-0.0033-0.0034-0.00060.003500.15760.0236-0.01290.1545-0.04340.2254-4.3686-21.204628.4404
300.0004-0.00010.00050.0002-0.00030.00040.0011-0.0042-0.0006-0.0024-0.0006-0.0028-0.00160.000500.1863-0.0044-0.01530.19160.00980.231231.831.4348-14.9605
310.00260.00060.00350.00130.0020.0051-0.0033-0.011-0.00060.00270.00730.0011-0.0007-0.00030.00150.06760.01830.00110.11920.03710.17710.767-20.966914.8797
320.0016-0.00130.00260.0014-0.00280.0045-0.00510.0064-0.0032-0.00950.004-0.0017-0.0022-0.0021-00.0806-0.0249-0.00070.182-0.03010.2428-0.6008-24.0098-2.4636
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 29 through 55 )A29 - 55
2X-RAY DIFFRACTION2chain 'A' and (resid 56 through 84 )A56 - 84
3X-RAY DIFFRACTION3chain 'A' and (resid 85 through 85 )A85
4X-RAY DIFFRACTION4chain 'B' and (resid 30 through 35 )B30 - 35
5X-RAY DIFFRACTION5chain 'B' and (resid 36 through 55 )B36 - 55
6X-RAY DIFFRACTION6chain 'B' and (resid 56 through 69 )B56 - 69
7X-RAY DIFFRACTION7chain 'B' and (resid 70 through 84 )B70 - 84
8X-RAY DIFFRACTION8chain 'C' and (resid 30 through 40 )C30 - 40
9X-RAY DIFFRACTION9chain 'C' and (resid 41 through 84 )C41 - 84
10X-RAY DIFFRACTION10chain 'D' and (resid 29 through 45 )D29 - 45
11X-RAY DIFFRACTION11chain 'D' and (resid 46 through 84 )D46 - 84
12X-RAY DIFFRACTION12chain 'E' and (resid 29 through 40 )E29 - 40
13X-RAY DIFFRACTION13chain 'E' and (resid 41 through 69 )E41 - 69
14X-RAY DIFFRACTION14chain 'E' and (resid 70 through 84 )E70 - 84
15X-RAY DIFFRACTION15chain 'F' and (resid 30 through 45 )F30 - 45
16X-RAY DIFFRACTION16chain 'F' and (resid 46 through 55 )F46 - 55
17X-RAY DIFFRACTION17chain 'F' and (resid 56 through 69 )F56 - 69
18X-RAY DIFFRACTION18chain 'F' and (resid 70 through 84 )F70 - 84
19X-RAY DIFFRACTION19chain 'G' and (resid 30 through 35 )G30 - 35
20X-RAY DIFFRACTION20chain 'G' and (resid 36 through 84 )G36 - 84
21X-RAY DIFFRACTION21chain 'H' and (resid 29 through 35 )H29 - 35
22X-RAY DIFFRACTION22chain 'H' and (resid 36 through 55 )H36 - 55
23X-RAY DIFFRACTION23chain 'H' and (resid 56 through 69 )H56 - 69
24X-RAY DIFFRACTION24chain 'H' and (resid 70 through 84 )H70 - 84
25X-RAY DIFFRACTION25chain 'J' and (resid 1 through 7 )J1 - 7
26X-RAY DIFFRACTION26chain 'I' and (resid 1 through 7 )I1 - 7
27X-RAY DIFFRACTION27chain 'K' and (resid 1 through 7 )K1 - 7
28X-RAY DIFFRACTION28chain 'L' and (resid 1 through 7 )L1 - 7
29X-RAY DIFFRACTION29chain 'M' and (resid 1 through 7 )M1 - 7
30X-RAY DIFFRACTION30chain 'N' and (resid 1 through 7 )N1 - 7
31X-RAY DIFFRACTION31chain 'O' and (resid 1 through 7 )O1 - 7
32X-RAY DIFFRACTION32chain 'P' and (resid 1 through 8 )P1 - 8

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Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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