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- PDB-4xid: AntpHD with 15bp DNA duplex -

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Basic information

Entry
Database: PDB / ID: 4xid
TitleAntpHD with 15bp DNA duplex
Components
  • DNA (5'-D(*AP*GP*AP*AP*AP*GP*CP*CP*AP*TP*TP*AP*GP*AP*G)-3')
  • DNA (5'-D(*TP*CP*TP*CP*TP*AP*AP*TP*GP*GP*CP*TP*TP*TP*C)-3')
  • Homeotic protein antennapediaHomeosis
KeywordsTranscription Regulator/DNA / HOMEODOMAIN / DNA-BINDING PROTEIN / COMPLEX (HOMEODOMAIN-DNA) / TRANSCRIPTION-DNA COMPLEX / Transcription Regulator-DNA complex
Function / homology
Function and homology information


specification of segmental identity, antennal segment / specification of segmental identity, thorax / neuroblast development / muscle cell fate specification / lymph gland development / ventral cord development / anterior/posterior axis specification / anterior/posterior pattern specification / midgut development / regulation of neurogenesis ...specification of segmental identity, antennal segment / specification of segmental identity, thorax / neuroblast development / muscle cell fate specification / lymph gland development / ventral cord development / anterior/posterior axis specification / anterior/posterior pattern specification / midgut development / regulation of neurogenesis / heart development / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / nucleus / cytoplasm
Similarity search - Function
Homeobox protein, antennapedia type / Homeobox protein, antennapedia type, conserved site / 'Homeobox' antennapedia-type protein signature. / Homeobox domain, metazoa / Homeobox, conserved site / 'Homeobox' domain signature. / Homeodomain / 'Homeobox' domain profile. / Homeodomain / Homeobox domain ...Homeobox protein, antennapedia type / Homeobox protein, antennapedia type, conserved site / 'Homeobox' antennapedia-type protein signature. / Homeobox domain, metazoa / Homeobox, conserved site / 'Homeobox' domain signature. / Homeodomain / 'Homeobox' domain profile. / Homeodomain / Homeobox domain / Homeodomain-like / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
NICKEL (II) ION / DNA / DNA (> 10) / Homeotic protein antennapedia
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
unidentified (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.701 Å
AuthorsWhite, M.A. / Zandarashvili, L. / Iwahara, J.
CitationJournal: Biophys.J. / Year: 2015
Title: Entropic Enhancement of Protein-DNA Affinity by Oxygen-to-Sulfur Substitution in DNA Phosphate.
Authors: Zandarashvili, L. / Nguyen, D. / Anderson, K.M. / White, M.A. / Gorenstein, D.G. / Iwahara, J.
History
DepositionJan 6, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 16, 2016Group: Data collection
Revision 1.2Nov 22, 2017Group: Derived calculations / Refinement description / Category: pdbx_struct_oper_list / software
Item: _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.3Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Homeotic protein antennapedia
B: DNA (5'-D(*AP*GP*AP*AP*AP*GP*CP*CP*AP*TP*TP*AP*GP*AP*G)-3')
C: DNA (5'-D(*TP*CP*TP*CP*TP*AP*AP*TP*GP*GP*CP*TP*TP*TP*C)-3')
D: Homeotic protein antennapedia
E: DNA (5'-D(*AP*GP*AP*AP*AP*GP*CP*CP*AP*TP*TP*AP*GP*AP*G)-3')
F: DNA (5'-D(*TP*CP*TP*CP*TP*AP*AP*TP*GP*GP*CP*TP*TP*TP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,68911
Polymers34,2776
Non-polymers4125
Water27015
1
A: Homeotic protein antennapedia
B: DNA (5'-D(*AP*GP*AP*AP*AP*GP*CP*CP*AP*TP*TP*AP*GP*AP*G)-3')
C: DNA (5'-D(*TP*CP*TP*CP*TP*AP*AP*TP*GP*GP*CP*TP*TP*TP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,3155
Polymers17,1383
Non-polymers1772
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3890 Å2
ΔGint-34 kcal/mol
Surface area8590 Å2
MethodPISA
2
D: Homeotic protein antennapedia
E: DNA (5'-D(*AP*GP*AP*AP*AP*GP*CP*CP*AP*TP*TP*AP*GP*AP*G)-3')
F: DNA (5'-D(*TP*CP*TP*CP*TP*AP*AP*TP*GP*GP*CP*TP*TP*TP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,3746
Polymers17,1383
Non-polymers2363
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3460 Å2
ΔGint-30 kcal/mol
Surface area8490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.443, 96.443, 90.142
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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Protein , 1 types, 2 molecules AD

#1: Protein Homeotic protein antennapedia / Homeosis


Mass: 7961.297 Da / Num. of mol.: 2 / Fragment: UNP residues 297-356
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Antp, CG1028 / Production host: Escherichia coli (E. coli) / References: UniProt: P02833

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DNA chain , 2 types, 4 molecules BECF

#2: DNA chain DNA (5'-D(*AP*GP*AP*AP*AP*GP*CP*CP*AP*TP*TP*AP*GP*AP*G)-3')


Mass: 4651.062 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) unidentified (others)
#3: DNA chain DNA (5'-D(*TP*CP*TP*CP*TP*AP*AP*TP*GP*GP*CP*TP*TP*TP*C)-3')


Mass: 4525.944 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) unidentified (others)

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Non-polymers , 3 types, 20 molecules

#4: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ni
#5: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H2O

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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: 3.13 Å3/Da / Density % sol: 60.75 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 20 mM BTP, 10 mM NiCl, 5% MPD / PH range: 7

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Data collection

DiffractionMean temperature: 85 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ DW / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Apr 25, 2014
RadiationMonochromator: Gradient Multilayer / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 12086 / % possible obs: 99 % / Redundancy: 7.8 % / Biso Wilson estimate: 74.86 Å2 / Rmerge(I) obs: 0.054 / Χ2: 1.254 / Net I/av σ(I): 35.671 / Net I/σ(I): 12.7 / Num. measured all: 94639
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Num. unique allΧ2% possible allRmerge(I) obs
2.7-2.7585740.89297.3
2.75-2.885840.9298.8
2.8-2.8585830.88798.3
2.85-2.9185890.93197.8
2.91-2.977.95950.9581000.868
2.97-3.048.15750.976980.618
3.04-3.1286011.08398.50.361
3.12-3.285901.21199.80.153
3.2-3.385871.38298.50.101
3.3-3.485971.42898.50.098
3.4-3.527.95901.333990.121
3.52-3.667.96071.37299.20.109
3.66-3.837.96021.42299.30.08
3.83-4.037.86071.44399.50.074
4.03-4.297.96081.43899.50.07
4.29-4.627.86101.58599.50.055
4.62-5.087.76261.51299.70.052
5.08-5.817.76181.52299.70.043
5.81-7.327.56451.53399.80.036
7.32-506.86981.21498.90.018

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: dev_1810)refinement
HKL-3000phasing
MOLREPphasing
PDB_EXTRACT3.15data extraction
Cootmodel building
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 9ANT
Resolution: 2.701→37.601 Å / SU ML: 0.6 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 35.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2743 2124 9.64 %Random selection
Rwork0.2236 ---
obs0.2285 12006 98.94 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.701→37.601 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1041 1218 19 15 2293
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052441
X-RAY DIFFRACTIONf_angle_d0.7463538
X-RAY DIFFRACTIONf_dihedral_angle_d29.0791010
X-RAY DIFFRACTIONf_chiral_restr0.036379
X-RAY DIFFRACTIONf_plane_restr0.003240
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7011-2.76390.48181510.46511323X-RAY DIFFRACTION98
2.7639-2.8330.41791370.40151306X-RAY DIFFRACTION98
2.833-2.90960.44681480.39291325X-RAY DIFFRACTION99
2.9096-2.99510.43711300.34621359X-RAY DIFFRACTION99
2.9951-3.09180.39711300.3051327X-RAY DIFFRACTION99
3.0918-3.20220.32761570.28571293X-RAY DIFFRACTION98
3.2022-3.33030.27961310.28431284X-RAY DIFFRACTION95
3.3303-3.48180.3361370.24691333X-RAY DIFFRACTION99
3.4818-3.66520.33091700.26351302X-RAY DIFFRACTION100
3.6652-3.89470.26631340.22731360X-RAY DIFFRACTION100
3.8947-4.1950.26011330.21051343X-RAY DIFFRACTION100
4.195-4.61650.27691660.18281308X-RAY DIFFRACTION100
4.6165-5.28290.1681120.17681380X-RAY DIFFRACTION100
5.2829-6.64990.22931320.19451340X-RAY DIFFRACTION100
6.6499-37.60460.22181560.17211336X-RAY DIFFRACTION100
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)
11.9324-0.17220.2631.7879-1.41471.1355-1.3069-0.1178-0.2948-1.38720.29170.2580.2624-0.4853-0.19171.84520.2248-0.38830.8247-0.25161.09967.3901-34.522918.1762
26.1664-0.75571.41832.3203-0.16750.35-0.1477-0.6054-0.10990.72360.1777-0.10491.9425-0.0214-0.36791.3285-0.02770.24250.35330.05160.4232-2.4147-27.484931.6956
30.4563-0.0358-0.28050.4446-0.12870.2136-0.3584-0.24450.7263-0.28550.20211.20090.5985-0.08790.00010.8510.0207-0.12370.6536-0.10960.87240.6006-15.406127.3186
41.7295-0.4078-1.65030.2907-0.7378.65350.3936-0.15321.2464-0.48521.0445-1.67611.31561.36090.56230.74520.07880.20450.4766-0.02380.73747.0401-23.205226.3667
50.2897-0.0175-0.00460.08840.17020.28970.38640.2130.05430.1556-0.211-0.23640.3864-0.8187-0.00330.9076-0.16170.06460.5647-0.06170.6157-3.4052-24.143921.2748
60.0366-0.00720.04290.1152-0.03360.04880.3909-0.8988-0.2430.40460.28451.18411.0145-0.434-0.00571.1603-0.47620.14351.33110.11841.1356-13.9211-26.952120.1513
70.14550.0904-0.08390.5366-0.64610.5890.3732-0.2460.1106-0.858-0.6222-0.47381.0672-0.2685-0.00220.7585-0.06140.07320.57610.00950.66161.8491-9.43412.2573
80.48320.42850.04341.9992-1.8722.2720.11610.3553-0.8848-2.0672-0.99-0.09840.5921-0.2423-0.48921.669-0.3788-0.15490.6396-0.13650.8215-5.8483-27.13249.2092
99.4559-3.50914.10286.1202-6.13366.20631.39621.037-2.70950.54070.778-0.74292.04160.72110.65692.00630.0161-0.28810.6885-0.07470.99924.7753-40.522915.2306
104.1404-5.04771.09476.1761-1.37151.0931.56910.7110.5353-0.5399-0.6864-0.0281.9474-0.4471-0.32391.4598-0.2425-0.36270.7425-0.28671.5128-3.543-45.784815.1711
116.04732.0076-4.61550.7525-1.28435.01930.37760.28992.1328-0.18190.18341.8420.0244-0.6990.33031.5604-0.05660.10350.6315-0.06580.94331.5464-30.021714.2715
120.6839-0.0610.52261.1092-0.1630.9459-0.0048-0.14280.4798-0.4593-0.42730.55480.0832-0.0677-0.00770.7142-0.1116-0.11830.6816-0.00680.5875-3.9707-13.26068.7012
130.3984-1.02380.28572.7372-1.29592.31960.04050.02790.14990.19380.5846-0.2452-0.86290.21180.28760.30730.0680.1970.93040.06960.409-14.91433.7443.3518
141.9796-0.22290.26080.0536-0.15690.80990.35041.2544-1.5215-0.05140.14020.0757-0.05760.25290.02530.5389-0.0084-0.02790.984-0.12750.5405-22.1989-6.338348.4376
150.5177-0.1107-0.0530.0309-0.12052.15610.24811.668-1.5581-1.1819-0.4626-0.3533-0.0163-2.08530.49140.6987-0.102-0.03681.7625-0.18791.3963-31.5051-5.624442.5511
161.22240.85231.39690.98310.20783.10650.27990.87930.8643-0.6901-0.44210.6265-0.7377-1.5932-0.42410.63450.46880.06581.67630.10320.6813-27.78934.858943.5171
176.8126-3.0030.5218.3833-5.59746.6657-0.38561.6430.5645-1.1364-1.052-0.21010.4843-1.2129-2.440.28830.1001-0.12211.7655-0.21060.5407-23.4888-3.667937.5805
182.54440.19654.07422.7205-1.55997.82121.43030.4888-1.20350.08090.5154-0.04741.1281-1.90930.19740.83990.12450.08691.7695-0.38311.3739-18.9472-15.186137.0747
190.6861-0.11060.50450.30770.45421.4042-0.5710.5481-0.6650.12810.63470.1956-0.34851.4928-0.10640.36980.19-0.50583.0762-0.09781.3735-40.28740.478627.8256
200.19130.0862-0.10340.6662-0.0930.1855-0.89111.3351-0.46310.25581.3079-1.79340.682-1.198-0.00410.87140.04260.02032.5273-0.34831.3775-26.017-9.113828.3536
213.1544-0.11225.01574.9344-1.24048.1561-0.43752.8271-0.1873-0.34061.7523-0.9129-1.8721-0.1711.65520.6741-0.1131-0.01211.77260.01250.6601-10.25340.451128.2449
221.8608-1.1461-0.52171.1975-0.11181.2419-0.78990.7035-0.2556-0.17910.3838-0.1288-0.5498-1.2062-0.08040.46750.01350.13961.0947-0.03760.7615-8.521-3.579332.3016
231.4055-0.98111.56350.7094-0.85795.396-0.52540.09030.096-0.84030.52111.6251-0.6759-2.17740.41390.82110.2657-0.57732.5431-0.05281.1729-25.4122-1.562222.4891
240.08870.021-0.10970.12330.01620.1266-1.18070.8413-0.66580.4053-0.0383-0.2671.01250.89670.00880.91130.30870.11552.0061-0.07210.8164-38.2066-8.12227.7987
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 3:7)
2X-RAY DIFFRACTION2(chain A and resid 8:23)
3X-RAY DIFFRACTION3(chain A and resid 24:33)
4X-RAY DIFFRACTION4(chain A and resid 34:45)
5X-RAY DIFFRACTION5(chain A and resid 46:53)
6X-RAY DIFFRACTION6(chain A and resid 54:60)
7X-RAY DIFFRACTION7(chain B and resid 0:5)
8X-RAY DIFFRACTION8(chain B and resid 6:10)
9X-RAY DIFFRACTION9(chain B and resid 11:14)
10X-RAY DIFFRACTION10(chain C and resid 24:27)
11X-RAY DIFFRACTION11(chain C and resid 28:32)
12X-RAY DIFFRACTION12(chain C and resid 33:38)
13X-RAY DIFFRACTION13(chain D and resid 5:13)
14X-RAY DIFFRACTION14(chain D and resid 14:22)
15X-RAY DIFFRACTION15(chain D and resid 23:29)
16X-RAY DIFFRACTION16(chain D and resid 30:43)
17X-RAY DIFFRACTION17(chain D and resid 44:53)
18X-RAY DIFFRACTION18(chain D and resid 54:60)
19X-RAY DIFFRACTION19(chain E and resid 0:4)
20X-RAY DIFFRACTION20(chain E and resid 5:8)
21X-RAY DIFFRACTION21(chain E and resid 9:14)
22X-RAY DIFFRACTION22(chain F and resid 24:30)
23X-RAY DIFFRACTION23(chain F and resid 31:34)
24X-RAY DIFFRACTION24(chain F and resid 35:38)

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  • 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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