[English] 日本語
Yorodumi
- PDB-7lky: Crystal Structure of PHF1 Tudor domain in complex with a peptidom... -

+
Open data


ID or keywords:

Loading...

-
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 methyltransferase binding / DNA repair-dependent chromatin remodeling / methylated histone binding / transcription corepressor binding / PRC2 methylates histones and DNA / site of double-strand break / chromatin organization / centrosome / chromatin binding / regulation of DNA-templated transcription ...histone methyltransferase binding / DNA repair-dependent chromatin remodeling / methylated histone binding / transcription corepressor binding / PRC2 methylates histones and DNA / site of double-strand break / chromatin organization / centrosome / chromatin binding / regulation of DNA-templated transcription / DNA binding / 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 / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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 / 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 / Water


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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

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

-
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

Read more