[English] 日本語
Yorodumi
- PDB-5uvf: Crystal Structure of the Human vaccinia-related kinase bound to B... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5uvf
TitleCrystal Structure of the Human vaccinia-related kinase bound to BI-D1870
ComponentsSerine/threonine-protein kinase VRK1
KeywordsTransferase/Transferase Inhibitor / transferase / protein kinase domain / Structural Genomics / Structural Genomics Consortium / SGC / Transferase-Transferase Inhibitor Complex
Function / homology
Function and homology information


histone H2AX kinase activity / Cajal body organization / Golgi disassembly / Nuclear Envelope Breakdown / positive regulation of protein localization to chromatin / mitotic nuclear membrane disassembly / regulation of neuron migration / Golgi stack / Initiation of Nuclear Envelope (NE) Reformation / nucleosomal DNA binding ...histone H2AX kinase activity / Cajal body organization / Golgi disassembly / Nuclear Envelope Breakdown / positive regulation of protein localization to chromatin / mitotic nuclear membrane disassembly / regulation of neuron migration / Golgi stack / Initiation of Nuclear Envelope (NE) Reformation / nucleosomal DNA binding / Cajal body / neuron projection development / kinase activity / protein autophosphorylation / histone binding / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / non-specific serine/threonine protein kinase / protein kinase activity / protein phosphorylation / chromatin remodeling / cell division / protein serine kinase activity / protein serine/threonine kinase activity / DNA damage response / protein kinase binding / nucleolus / chromatin / signal transduction / nucleoplasm / ATP binding / nucleus / cytosol
Similarity search - Function
: / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. ...: / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-7DZ / DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / Serine/threonine-protein kinase VRK1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsCounago, R.M. / Bountra, C. / Arruda, P. / Edwards, A.M. / Gileadi, O. / Structural Genomics Consortium (SGC)
Funding support Brazil, 1items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)13/50724-5 Brazil
CitationJournal: Sci Rep / Year: 2017
Title: Structural characterization of human Vaccinia-Related Kinases (VRK) bound to small-molecule inhibitors identifies different P-loop conformations.
Authors: Counago, R.M. / Allerston, C.K. / Savitsky, P. / Azevedo, H. / Godoi, P.H. / Wells, C.I. / Mascarello, A. / de Souza Gama, F.H. / Massirer, K.B. / Zuercher, W.J. / Guimaraes, C.R.W. / Gileadi, O.
History
DepositionFeb 20, 2017Deposition site: RCSB / Processing site: RCSB
SupersessionMar 22, 2017ID: 5UGE
Revision 1.0Mar 22, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 4, 2018Group: Author supporting evidence / Data collection / Database references
Category: citation / citation_author ...citation / citation_author / diffrn_source / pdbx_audit_support
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _diffrn_source.pdbx_synchrotron_site / _pdbx_audit_support.grant_number
Revision 1.2Apr 17, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Serine/threonine-protein kinase VRK1
B: Serine/threonine-protein kinase VRK1
C: Serine/threonine-protein kinase VRK1
D: Serine/threonine-protein kinase VRK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)167,20920
Polymers164,5534
Non-polymers2,65716
Water12,304683
1
A: Serine/threonine-protein kinase VRK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,7194
Polymers41,1381
Non-polymers5813
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Serine/threonine-protein kinase VRK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,6253
Polymers41,1381
Non-polymers4862
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Serine/threonine-protein kinase VRK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0518
Polymers41,1381
Non-polymers9137
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Serine/threonine-protein kinase VRK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,8145
Polymers41,1381
Non-polymers6764
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)92.141, 95.242, 192.040
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 1 types, 4 molecules ABCD

#1: Protein
Serine/threonine-protein kinase VRK1 / Vaccinia-related kinase 1


Mass: 41138.125 Da / Num. of mol.: 4 / Fragment: UNP RESIDUES 3-364 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VRK1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): DE3 / Variant (production host): R3
References: UniProt: Q99986, non-specific serine/threonine protein kinase

-
Non-polymers , 5 types, 699 molecules

#2: Chemical
ChemComp-7DZ / (7S)-2-[(3,5-difluoro-4-hydroxyphenyl)amino]-5,7-dimethyl-8-(3-methylbutyl)-7,8-dihydropteridin-6(5H)-one / BI-D1870


Mass: 391.415 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C19H23F2N5O2
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 683 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.56 Å3/Da / Density % sol: 51.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 25% PEG3350, 0.1M BISTRIS, 0.2M, LITHIUM SULFATE, PH 6.5
PH range: 6.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Aug 5, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.8→29.66 Å / Num. obs: 156295 / % possible obs: 99.7 % / Redundancy: 6.2 % / Biso Wilson estimate: 41.72 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 12.5
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 3.7 % / Rmerge(I) obs: 1.943 / Mean I/σ(I) obs: 0.5 / % possible all: 96.8

-
Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3OP5

3op5


Resolution: 2→29.66 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.939 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.136 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.139 / SU Rfree Blow DPI: 0.127 / SU Rfree Cruickshank DPI: 0.126
RfactorNum. reflection% reflectionSelection details
Rfree0.204 5538 4.99 %RANDOM
Rwork0.173 ---
obs0.175 110975 96.8 %-
Displacement parametersBiso mean: 52.86 Å2
Baniso -1Baniso -2Baniso -3
1-1.6299 Å20 Å20 Å2
2---12.1543 Å20 Å2
3---10.5244 Å2
Refine analyzeLuzzati coordinate error obs: 0.23 Å
Refinement stepCycle: LAST / Resolution: 2→29.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9597 0 170 683 10450
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.019995HARMONIC2
X-RAY DIFFRACTIONt_angle_deg113574HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3430SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes221HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1458HARMONIC5
X-RAY DIFFRACTIONt_it9995HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.25
X-RAY DIFFRACTIONt_other_torsion16.23
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1264SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact12016SEMIHARMONIC4
LS refinement shellResolution: 2→2.05 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.236 381 4.6 %
Rwork0.204 7901 -
all0.205 8282 -
obs--98.94 %
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)
13.158-1.28570.24654.63982.71626.35310.0974-0.13440.22320.04670.3247-0.7003-0.29260.5357-0.4221-0.0809-0.05390.08290.1185-0.0499-0.088535.3881-3.28793.7792
24.94320.5311-0.091.60954.50633.6799-0.01910.52290.2841-0.44140.352-0.5437-0.78160.2374-0.3329-0.0728-0.07470.12060.007-0.0976-0.118833.5522-1.54145.6345
35.1095-2.83710.64476.38931.51790.41560.12190.3557-0.1693-0.8573-0.2460.3136-0.3908-0.29910.12420.13280.10510.0150.0649-0.0355-0.208315.539-5.556710.5673
40.717-0.4679-0.73982.12271.61342.25660.14450.14130.1451-0.1947-0.1209-0.196-0.4036-0.0757-0.02360.03690.01990.03430.0116-0.0167-0.109920.07923.308116.2202
51.49130.49810.05872.95141.18593.539-0.02110.026-0.10530.2388-0.083-0.13690.3707-0.13190.1041-0.00550.01370.0564-0.0448-0.0667-0.188714.7902-2.610530.6239
62.2224-0.1888-0.13142.2359-0.08662.8221-0.0564-0.12740.2350.350.0376-0.1331-0.29970.0750.01880.1255-0.0060.0188-0.0969-0.0631-0.154315.39759.073641.3309
71.5416-0.3922-0.05774.3067-0.07562.9983-0.0119-0.05180.2342-0.2347-0.30260.4111-0.3248-0.58160.3145-0.04410.1181-0.00050.0979-0.1648-0.11354.33439.519825.1525
82.56140.89741.17263.36212.69854.1286-0.10870.051-0.40730.15950.10070.16250.856-0.22270.00810.1615-0.10840.01-0.21770.0691-0.1714-18.1872-61.599645.2584
91.7222-1.06982.72814.8726-1.26174.7970.1685-0.187-0.49530.3469-0.07270.30010.8398-0.4557-0.09580.142-0.2055-0.0398-0.15040.0348-0.07-19.486-60.083642.4053
102.8553-0.33670.85822.59980.33042.859-0.0613-0.224-0.03920.2652-0.02150.0630.1109-0.08220.0828-0.013-0.0401-0.0142-0.05040.0325-0.1915-16.6961-42.927137.9149
113.55590.30592.26920.0134-0.57743.1346-0.0009-0.3033-0.21620.05990.04010.20420.3369-0.3554-0.0393-0.0005-0.05430.0571-0.08670.0315-0.1953-19.7708-47.564940.4678
121.6434-0.26550.66791.5918-0.62862.1028-0.0215-0.0694-0.388-0.02030.14220.19620.6329-0.5723-0.12070.1124-0.20140.01250.05160.0288-0.0488-27.9055-55.542531.7415
132.4387-0.23830.61521.149-0.26373.2867-0.0913-0.1398-0.07570.20580.05340.19980.1292-0.47410.0379-0.0277-0.0591-0.00280.03540.0066-0.1006-26.7952-42.856730.2054
145.84471.3009-1.011700.43222.5571-0.06980.2996-0.4546-0.0120.0377-0.40590.11560.5050.0321-0.051-0.0492-0.10350.18310.0402-0.058-10.1301-40.541219.2133
151.1352-0.10671.16150.38110.06913.14730.00560.1526-0.0425-0.04070.0350.13590.1496-0.2362-0.0407-0.0668-0.051-0.05290.0122-0.0011-0.1216-26.428-42.449816.8369
162.6899-0.5455-0.08661.5783-0.55852.0664-0.0270.3897-0.1065-0.207-0.00780.34040.1788-0.72140.0348-0.057-0.0787-0.09720.219-0.0237-0.0826-33.9545-42.75217.9944
175.6046-1.66571.13992.3163-0.6494.8056-0.06380.11990.2756-0.0487-0.06650.2041-0.2652-0.32630.1304-0.1115-0.0049-0.094-0.09020.0277-0.1292-27.4192-30.678217.9391
180.9353-1.0751-1.52671.2757-1.50144.31720.0425-0.39130.33690.14120.0870.5355-0.3627-0.8794-0.1295-0.12370.1012-0.0180.2329-0.0126-0.0589-38.8994-33.047629.3823
196.5108-1.2569-0.11776.01140.71421.7143-0.3040.26770.1788-0.19410.31450.971-0.0219-0.2497-0.0104-0.1075-0.0326-0.0987-0.16870.0922-0.0948-23.249111.187243.1146
202.10690.23350.10391.9025-0.37561.1905-0.04220.1294-0.0675-0.10080.06790.42760.0864-0.2342-0.0257-0.0391-0.0206-0.0124-0.1362-0.0032-0.0957-17.53883.703350.083
211.63510.1253-0.06990.9145-0.17171.8833-0.039-0.2388-0.3560.0594-0.00770.1080.2196-0.07970.04670.04110.00130.0171-0.1090.0451-0.0483-7.8547-4.108960.9279
223.9661-0.90932.41554.80550.87332.7425-0.0191-0.13970.55990.1262-0.0411-0.0504-0.4686-0.26610.06020.29210.29050.3555-0.2929-0.03620.176-36.47989.40977.9055
231.53230.7926-2.73872.2658-0.93920.2021-0.02190.25120.59570.06440.48570.5675-0.352-0.855-0.4639-0.1530.14330.06720.02810.1026-0.0409-39.4203-2.77130.9031
244.82390.96070.5184.1714-0.99227.340.2175-0.73990.0790.70740.0203-0.09210.059-0.0917-0.2379-0.0830.025-0.0115-0.0307-0.0422-0.1881-29.2303-14.034712.7794
252.55850.1998-1.87381.3204-0.76884.01840.2273-0.2310.52210.29140.0964-0.0181-0.64840.1936-0.3236-0.04040.00650.0354-0.0159-0.0792-0.0162-24.1562-6.05171.852
261.67690.13190.13081.11570.04792.6555-0.06020.13530.0655-0.0820.10590.0859-0.0347-0.2549-0.0458-0.12630.0215-0.00050.0690.0239-0.0736-30.3103-15.3695-10.2978
274.7781-0.73661.56042.2302-0.51983.9215-0.02950.47190.0088-0.3323-0.0447-0.19580.12490.38970.0742-0.1283-0.02510.07140.1218-0.0005-0.0824-15.7366-15.8285-19.308
282.75860.7673-0.61181.89170.10842.785-0.1184-0.492-0.08690.06810.0453-0.23740.27980.44220.0732-0.15120.1088-0.02970.1014-0.0388-0.0989-16.8415-22.5066-1.0489
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{A|20 - 56}
2X-RAY DIFFRACTION2{A|57 - 77}
3X-RAY DIFFRACTION3{A|78 - 103}
4X-RAY DIFFRACTION4{A|104 - 205}
5X-RAY DIFFRACTION5{A|206 - 256}
6X-RAY DIFFRACTION6{A|257 - 296}
7X-RAY DIFFRACTION7{A|297 - 341}
8X-RAY DIFFRACTION8{B|22 - 56}
9X-RAY DIFFRACTION9{B|57 - 77}
10X-RAY DIFFRACTION10{B|78 - 102}
11X-RAY DIFFRACTION11{B|103 - 121}
12X-RAY DIFFRACTION12{B|122 - 150}
13X-RAY DIFFRACTION13{B|151 - 205}
14X-RAY DIFFRACTION14{B|206 - 223}
15X-RAY DIFFRACTION15{B|224 - 256}
16X-RAY DIFFRACTION16{B|257 - 296}
17X-RAY DIFFRACTION17{B|297 - 316}
18X-RAY DIFFRACTION18{B|317 - 341}
19X-RAY DIFFRACTION19{C|30 - 112}
20X-RAY DIFFRACTION20{C|113 - 216}
21X-RAY DIFFRACTION21{C|217 - 341}
22X-RAY DIFFRACTION22{D|26 - 67}
23X-RAY DIFFRACTION23{D|68 - 90}
24X-RAY DIFFRACTION24{D|91 - 112}
25X-RAY DIFFRACTION25{D|113 - 195}
26X-RAY DIFFRACTION26{D|196 - 256}
27X-RAY DIFFRACTION27{D|257 - 296}
28X-RAY DIFFRACTION28{D|297 - 341}

+
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