[English] 日本語
Yorodumi
- PDB-7fj2: Structure of FOXM1 homodimer bound to a palindromic DNA site -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7fj2
TitleStructure of FOXM1 homodimer bound to a palindromic DNA site
Components
  • DNA (5'-D(*AP*CP*CP*GP*TP*AP*AP*AP*CP*AP*TP*GP*TP*TP*TP*AP*CP*GP*GP*T)-3')
  • Forkhead box protein M1
KeywordsTRANSCRIPTION / Forkhead transcription factors / FOXM1 / Dimer / DNA binding
Function / homology
Function and homology information


regulation of Ras protein signal transduction / Polo-like kinase mediated events / regulation of reactive oxygen species metabolic process / positive regulation of double-strand break repair / negative regulation of stress-activated MAPK cascade / DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / Cyclin A/B1/B2 associated events during G2/M transition / regulation of cell growth / RNA polymerase II transcription regulatory region sequence-specific DNA binding / G2/M transition of mitotic cell cycle ...regulation of Ras protein signal transduction / Polo-like kinase mediated events / regulation of reactive oxygen species metabolic process / positive regulation of double-strand break repair / negative regulation of stress-activated MAPK cascade / DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / Cyclin A/B1/B2 associated events during G2/M transition / regulation of cell growth / RNA polymerase II transcription regulatory region sequence-specific DNA binding / G2/M transition of mitotic cell cycle / regulation of cell population proliferation / DNA-binding transcription factor activity, RNA polymerase II-specific / regulation of cell cycle / DNA-binding transcription factor activity / DNA repair / negative regulation of DNA-templated transcription / positive regulation of cell population proliferation / chromatin / regulation of transcription by RNA polymerase II / protein kinase binding / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus
Similarity search - Function
: / Forkhead box protein M1 / Fork head domain conserved site1 / Fork head domain signature 1. / Fork head domain / Forkhead domain / Fork head domain profile. / FORKHEAD / Fork head domain conserved site 2 / Fork head domain signature 2. ...: / Forkhead box protein M1 / Fork head domain conserved site1 / Fork head domain signature 1. / Fork head domain / Forkhead domain / Fork head domain profile. / FORKHEAD / Fork head domain conserved site 2 / Fork head domain signature 2. / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / Forkhead box protein M1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.098 Å
AuthorsDai, S.Y. / Li, J. / Zhang, H.J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81570537 China
CitationJournal: J.Mol.Biol. / Year: 2021
Title: Mechanistic Insights into the Preference for Tandem Binding Sites in DNA Recognition by FOXM1.
Authors: Zhang, H. / Dai, S. / Liang, X. / Li, J. / Chen, Y.
History
DepositionAug 2, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 26, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Forkhead box protein M1
B: Forkhead box protein M1
C: DNA (5'-D(*AP*CP*CP*GP*TP*AP*AP*AP*CP*AP*TP*GP*TP*TP*TP*AP*CP*GP*GP*T)-3')
D: DNA (5'-D(*AP*CP*CP*GP*TP*AP*AP*AP*CP*AP*TP*GP*TP*TP*TP*AP*CP*GP*GP*T)-3')
E: Forkhead box protein M1
F: Forkhead box protein M1
G: DNA (5'-D(*AP*CP*CP*GP*TP*AP*AP*AP*CP*AP*TP*GP*TP*TP*TP*AP*CP*GP*GP*T)-3')
H: DNA (5'-D(*AP*CP*CP*GP*TP*AP*AP*AP*CP*AP*TP*GP*TP*TP*TP*AP*CP*GP*GP*T)-3')


Theoretical massNumber of molelcules
Total (without water)79,2548
Polymers79,2548
Non-polymers00
Water00
1
A: Forkhead box protein M1
B: Forkhead box protein M1
C: DNA (5'-D(*AP*CP*CP*GP*TP*AP*AP*AP*CP*AP*TP*GP*TP*TP*TP*AP*CP*GP*GP*T)-3')
D: DNA (5'-D(*AP*CP*CP*GP*TP*AP*AP*AP*CP*AP*TP*GP*TP*TP*TP*AP*CP*GP*GP*T)-3')


Theoretical massNumber of molelcules
Total (without water)39,6274
Polymers39,6274
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5490 Å2
ΔGint-37 kcal/mol
Surface area13800 Å2
MethodPISA
2
E: Forkhead box protein M1
F: Forkhead box protein M1
G: DNA (5'-D(*AP*CP*CP*GP*TP*AP*AP*AP*CP*AP*TP*GP*TP*TP*TP*AP*CP*GP*GP*T)-3')
H: DNA (5'-D(*AP*CP*CP*GP*TP*AP*AP*AP*CP*AP*TP*GP*TP*TP*TP*AP*CP*GP*GP*T)-3')


Theoretical massNumber of molelcules
Total (without water)39,6274
Polymers39,6274
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5460 Å2
ΔGint-37 kcal/mol
Surface area14180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.387, 45.456, 133.591
Angle α, β, γ (deg.)90.000, 92.850, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain C
21chain D
31chain G
41chain H
12(chain A and (resid 236 through 273 or (resid 274...
22(chain B and (resid 236 through 252 or (resid 253...
32(chain E and (resid 236 through 273 or (resid 274...
42(chain F and (resid 236 through 252 or (resid 253...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111DADADTDTchain CCC7 - 261 - 20
211DADADTDTchain DDD7 - 261 - 20
311DADADTDTchain GGG7 - 261 - 20
411DADADTDTchain HHH7 - 261 - 20
112ARGARGPHEPHE(chain A and (resid 236 through 273 or (resid 274...AA236 - 27316 - 53
122LYSLYSLYSLYS(chain A and (resid 236 through 273 or (resid 274...AA27454
132VALVALHISHIS(chain A and (resid 236 through 273 or (resid 274...AA233 - 31113 - 91
142VALVALHISHIS(chain A and (resid 236 through 273 or (resid 274...AA233 - 31113 - 91
152VALVALHISHIS(chain A and (resid 236 through 273 or (resid 274...AA233 - 31113 - 91
162VALVALHISHIS(chain A and (resid 236 through 273 or (resid 274...AA233 - 31113 - 91
212ARGARGTHRTHR(chain B and (resid 236 through 252 or (resid 253...BB236 - 25216 - 32
222GLUGLUARGARG(chain B and (resid 236 through 252 or (resid 253...BB253 - 25433 - 34
232ARGARGHISHIS(chain B and (resid 236 through 252 or (resid 253...BB236 - 31116 - 91
242ARGARGHISHIS(chain B and (resid 236 through 252 or (resid 253...BB236 - 31116 - 91
252ARGARGHISHIS(chain B and (resid 236 through 252 or (resid 253...BB236 - 31116 - 91
262ARGARGHISHIS(chain B and (resid 236 through 252 or (resid 253...BB236 - 31116 - 91
312ARGARGPHEPHE(chain E and (resid 236 through 273 or (resid 274...EE236 - 27316 - 53
322LYSLYSLYSLYS(chain E and (resid 236 through 273 or (resid 274...EE27454
332VALVALHISHIS(chain E and (resid 236 through 273 or (resid 274...EE233 - 31113 - 91
342VALVALHISHIS(chain E and (resid 236 through 273 or (resid 274...EE233 - 31113 - 91
352VALVALHISHIS(chain E and (resid 236 through 273 or (resid 274...EE233 - 31113 - 91
362VALVALHISHIS(chain E and (resid 236 through 273 or (resid 274...EE233 - 31113 - 91
412ARGARGTHRTHR(chain F and (resid 236 through 252 or (resid 253...FF236 - 25216 - 32
422GLUGLUARGARG(chain F and (resid 236 through 252 or (resid 253...FF253 - 25433 - 34
432SERSERHISHIS(chain F and (resid 236 through 252 or (resid 253...FF232 - 31112 - 91
442SERSERHISHIS(chain F and (resid 236 through 252 or (resid 253...FF232 - 31112 - 91
452SERSERHISHIS(chain F and (resid 236 through 252 or (resid 253...FF232 - 31112 - 91
462SERSERHISHIS(chain F and (resid 236 through 252 or (resid 253...FF232 - 31112 - 91

NCS ensembles :
ID
1
2

-
Components

#1: Protein
Forkhead box protein M1


Mass: 13680.487 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FOXM1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q08050
#2: DNA chain
DNA (5'-D(*AP*CP*CP*GP*TP*AP*AP*AP*CP*AP*TP*GP*TP*TP*TP*AP*CP*GP*GP*T)-3')


Mass: 6132.991 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.65 Å3/Da / Density % sol: 53.67 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I_PLUS/MINUS COLUMNS.
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.7
Details: 50 mM Sodium acetate pH 4.7 250 mM Sodium chloride 15% PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.58 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Dec 20, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.58 Å / Relative weight: 1
ReflectionResolution: 3.098→49.303 Å / Num. obs: 12865 / % possible obs: 87.7 % / Redundancy: 5.2 % / Biso Wilson estimate: 73.27 Å2 / CC1/2: 0.978 / CC star: 0.994 / Net I/σ(I): 10.1
Reflection shellResolution: 3.1→3.2 Å / Num. unique obs: 810 / CC1/2: 0.946

-
Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.27data extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3G73
Resolution: 3.098→49.303 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2654 1274 9.91 %
Rwork0.216 11578 -
obs0.2208 12852 82.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 96.65 Å2 / Biso mean: 65.6844 Å2 / Biso min: 44.72 Å2
Refinement stepCycle: final / Resolution: 3.098→49.303 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2556 1624 0 0 4180
Num. residues----394
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084464
X-RAY DIFFRACTIONf_angle_d0.9046400
X-RAY DIFFRACTIONf_chiral_restr0.05691
X-RAY DIFFRACTIONf_plane_restr0.007529
X-RAY DIFFRACTIONf_dihedral_angle_d20.4652308
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11C780X-RAY DIFFRACTION8.624TORSIONAL
12D780X-RAY DIFFRACTION8.624TORSIONAL
13G780X-RAY DIFFRACTION8.624TORSIONAL
14H780X-RAY DIFFRACTION8.624TORSIONAL
21A1435X-RAY DIFFRACTION8.624TORSIONAL
22B1435X-RAY DIFFRACTION8.624TORSIONAL
23E1435X-RAY DIFFRACTION8.624TORSIONAL
24F1435X-RAY DIFFRACTION8.624TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.098-3.22160.401910.314680153
3.2216-3.36820.30551070.281396162
3.3682-3.54580.30941240.2608108971
3.5458-3.76780.29381360.2552127381
3.7678-4.05860.27141460.2324136188
4.0586-4.46680.24221600.2013145494
4.4668-5.11260.2661610.2002152897
5.1126-6.43910.24571800.1915155698
6.4391-49.3030.24331690.197155595
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.550.1299-0.14190.1247-0.15080.09970.4781-0.77780.75960.5404-0.56260.13150.25361.39760.01750.7430.0540.10540.824-0.32960.5871-54.170310.7-21.5468
20.0527-0.05680.08630.17770.40650.86410.0468-0.5506-0.43120.98020.1335-0.171-0.81310.5637-0.00010.6079-0.0188-0.04440.6751-0.05520.6196-42.935715.0133-30.8085
30.6813-0.77480.11190.8325-0.12660.01250.5088-0.43120.0567-0.20850.1803-0.301-0.35320.54330.00230.58390.1345-0.02450.72020.00250.6233-42.16676.2378-31.0272
40.8003-0.3390.24590.38780.15250.50950.1545-0.614-0.5482-0.4485-0.01480.2012-0.1231-0.8668-0.00010.5488-0.04040.01780.6125-0.02240.6037-52.56655.8689-32.4727
50.2246-0.1074-0.19470.1855-0.27750.7862-0.90050.6411-0.77830.3080.51851.55630.2954-0.2237-0.00420.7301-0.04870.07860.52420.10290.6705-43.301116.2975-42.0655
65.2134-1.6834-0.39069.6677-0.96190.16961.18530.3652-0.55040.69280.73870.8465-0.50920.86020.61470.69230.0057-0.68610.6681-0.022-0.6898-36.222510.5643-42.1304
72.0025-3.20843.86055.4898-5.5189.2758-0.53860.46780.2727-0.3627-0.7182-1.5781-1.0643-0.3259-2.06370.75360.14160.08560.1814-0.39750.9893-37.6575-6.0879-72.2042
82.0028-1.6459-0.53231.7772-0.41060.18320.34612.03631.1793-0.40910.3486-0.62880.42630.0870.08420.82230.01910.02180.5752-0.13750.252-34.61031.8431-65.8925
90.76790.5648-0.34490.327-0.32880.74790.4210.15480.5510.30080.11711.218-0.2376-0.28380.01290.55080.0264-0.09880.56560.07720.4637-42.45285.3258-67.1367
100.89920.1141-1.25331.1595-0.11251.5336-0.077-0.1758-0.27841.0477-0.2407-0.19910.4194-0.2632-0.04550.7862-0.05680.10360.57620.03480.4111-38.7741-0.6259-56.8971
110.0972-0.025-0.13680.10390.15940.17840.39630.16450.34080.088-0.1337-0.2826-0.0079-0.2076-0.00040.68180.02040.11330.4241-0.06890.3518-36.716711.4762-53.8282
120.87881.1545-0.1231.25140.2334-0.04790.08820.49720.13650.346-0.49860.1882-0.0444-1.1926-0.00120.82610.08710.04290.746-0.00010.8815-59.750510.1486-41.4708
130.21731.30510.4012.18711.11340.16970.01310.2978-0.07450.03020.0941-0.55260.2111-0.2065-0.00090.80960.04050.02970.49210.02060.5125-41.6744-11.5076-54.4893
140.1774-0.1190.09010.12110.0530.1239-0.9326-1.8343-0.2020.45380.91370.63120.0092-0.4576-0.00120.98990.06790.0540.71320.01860.592-36.4772-13.7046-61.1058
15-0.0309-0.20990.18250.6175-0.42650.215-0.16940.20450.32210.4263-0.20710.46870.3527-0.2086-0.00020.701-0.03380.03750.5616-0.07380.6428-50.38850.1497-48.2337
160.2209-0.0516-0.22290.01080.14560.24961.54370.81761.5570.54690.5836-0.6787-0.7793-0.00360.00480.77360.1506-0.01141.2793-0.22491.0112-68.188714.4387-37.8804
171.79771.32650.33591.5496-0.24810.38870.05471.3432-1.5767-0.1466-0.3282-1.3056-0.6532-0.42940.03250.8880.1310.25130.80510.05230.667112.7089-9.6071-18.5874
181.0676-1.5278-2.90863.1843.07912.00770.4622-0.447-0.9831-0.56360.0206-0.0744-0.59211.19651.2215-0.15820.2542-0.3390.72960.20761.10762.9258-14.1804-8.1919
190.78820.87310.00751.1522-0.31440.2431-0.2037-0.2610.35330.7110.0838-0.5761-0.91920.7317-0.00110.4862-0.0537-0.12030.89480.07210.49264.8904-3.9697-10.8943
200.0592-0.07670.08030.41710.04980.175-0.53670.50820.93870.98040.8437-0.60380.317-0.4265-0.00290.43170.0565-0.0620.54540.06330.9886-3.3829-7.2714-18.1192
210.72350.21090.22170.09080.36381.26050.01410.0211-0.1271-0.01470.19130.25931.1145-0.42570.0390.6099-0.06780.06370.67690.27531.1838-8.2403-15.7427-9.2747
220.0981-0.39310.05991.1782-0.26610.0276-0.70590.11710.7559-1.16960.7206-0.91820.6288-0.635-0.00470.397-0.03530.04930.6826-0.14760.8408-8.9356-10.0052-2.502
232.0191.94631.96510.35850.6623.0788-0.95471.18091.6580.6294-0.3695-1.26790.2907-0.3003-0.6120.50210.2035-0.04570.5124-0.12280.5996-42.2027.7103-10.5381
243.22020.0517-1.01870.6743-1.19981.8705-0.1655-0.0236-0.2153-0.41330.0639-0.26410.3708-0.37720.00050.34410.0044-0.0620.47010.03370.4105-31.5666-2.0744-9.2591
250.4177-0.78220.91221.4916-1.73932.01380.0899-0.4032-0.19311.2511-0.8487-0.8222-0.64811.1064-0.18740.5574-0.075-0.07220.64570.30810.8993-21.9072-3.1928-0.0135
260.08170.0772-0.06250.0649-0.02140.0076-0.3498-0.0776-0.5449-0.0973-0.0640.33620.54490.38260.00090.37430.00410.06880.4560.07890.4657-21.154-10.9526-3.9353
270.5991-0.1828-0.63910.6338-0.791.01180.28220.54060.46640.2672-0.2067-0.42540.258-0.3151-0.00050.92220.08820.17030.71360.02360.6151-6.6602-9.5192-25.8549
280.1898-0.50850.25882.1561-1.62990.7892-0.35680.61890.32060.32560.1052-0.4970.0947-0.67990.00010.5773-0.0250.03460.6286-0.02910.8808-21.095111.9013-8.5268
290.1484-0.0862-0.45440.1981-0.24780.7777-0.0516-0.25850.84640.1255-0.2242-0.19760.26510.10370.00060.4732-0.04920.05970.584-0.01090.7171-21.775111.5165-9.9227
301.64750.8629-2.46430.4312-1.30882.3954-0.3140.63160.35450.21630.1615-0.65930.4583-0.1826-0.00070.68970.15320.06780.7404-0.00910.7535-7.3832-11.0169-26.2744
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 233 through 240 )A233 - 240
2X-RAY DIFFRACTION2chain 'A' and (resid 241 through 255 )A241 - 255
3X-RAY DIFFRACTION3chain 'A' and (resid 256 through 269 )A256 - 269
4X-RAY DIFFRACTION4chain 'A' and (resid 270 through 291 )A270 - 291
5X-RAY DIFFRACTION5chain 'A' and (resid 292 through 299 )A292 - 299
6X-RAY DIFFRACTION6chain 'A' and (resid 300 through 311 )A300 - 311
7X-RAY DIFFRACTION7chain 'B' and (resid 236 through 240 )B236 - 240
8X-RAY DIFFRACTION8chain 'B' and (resid 241 through 251 )B241 - 251
9X-RAY DIFFRACTION9chain 'B' and (resid 252 through 278 )B252 - 278
10X-RAY DIFFRACTION10chain 'B' and (resid 279 through 299 )B279 - 299
11X-RAY DIFFRACTION11chain 'B' and (resid 300 through 311 )B300 - 311
12X-RAY DIFFRACTION12chain 'C' and (resid 7 through 16 )C7 - 16
13X-RAY DIFFRACTION13chain 'C' and (resid 17 through 26 )C17 - 26
14X-RAY DIFFRACTION14chain 'D' and (resid 7 through 11 )D7 - 11
15X-RAY DIFFRACTION15chain 'D' and (resid 12 through 21 )D12 - 21
16X-RAY DIFFRACTION16chain 'D' and (resid 22 through 26 )D22 - 26
17X-RAY DIFFRACTION17chain 'E' and (resid 233 through 240 )E233 - 240
18X-RAY DIFFRACTION18chain 'E' and (resid 241 through 255 )E241 - 255
19X-RAY DIFFRACTION19chain 'E' and (resid 256 through 278 )E256 - 278
20X-RAY DIFFRACTION20chain 'E' and (resid 279 through 291 )E279 - 291
21X-RAY DIFFRACTION21chain 'E' and (resid 292 through 299 )E292 - 299
22X-RAY DIFFRACTION22chain 'E' and (resid 300 through 311 )E300 - 311
23X-RAY DIFFRACTION23chain 'F' and (resid 232 through 240 )F232 - 240
24X-RAY DIFFRACTION24chain 'F' and (resid 241 through 291 )F241 - 291
25X-RAY DIFFRACTION25chain 'F' and (resid 292 through 299 )F292 - 299
26X-RAY DIFFRACTION26chain 'F' and (resid 300 through 311 )F300 - 311
27X-RAY DIFFRACTION27chain 'G' and (resid 7 through 16 )G7 - 16
28X-RAY DIFFRACTION28chain 'G' and (resid 17 through 26 )G17 - 26
29X-RAY DIFFRACTION29chain 'H' and (resid 7 through 16 )H7 - 16
30X-RAY DIFFRACTION30chain 'H' and (resid 17 through 26 )H17 - 26

+
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://pdbjlvh1.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