[English] 日本語
Yorodumi
- PDB-4cym: Complex of human VARP-ANKRD1 with Rab32-GppCp -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4cym
TitleComplex of human VARP-ANKRD1 with Rab32-GppCp
Components
  • ANKYRIN REPEAT DOMAIN-CONTAINING PROTEIN 27
  • RAS-RELATED PROTEIN RAB-32
KeywordsTRANSPORT PROTEIN / VARP / RAB-EFFECTOR / RAB / ENDOSOME / VESICLE TRAFFICKING / MELANOSOME BIOGENESIS
Function / homology
Function and homology information


BLOC-2 complex binding / AP-3 adaptor complex binding / AP-1 adaptor complex binding / negative regulation of SNARE complex assembly / tubular endosome / endosome to melanosome transport / phagosome maturation / mitochondria-associated endoplasmic reticulum membrane contact site / melanosome assembly / melanosome organization ...BLOC-2 complex binding / AP-3 adaptor complex binding / AP-1 adaptor complex binding / negative regulation of SNARE complex assembly / tubular endosome / endosome to melanosome transport / phagosome maturation / mitochondria-associated endoplasmic reticulum membrane contact site / melanosome assembly / melanosome organization / melanosome membrane / GTP-dependent protein binding / RAB geranylgeranylation / early endosome to late endosome transport / RAB GEFs exchange GTP for GDP on RABs / endocytic recycling / protein localization to membrane / positive regulation of dendrite morphogenesis / antigen processing and presentation / endomembrane system / phagocytic vesicle / transport vesicle / vesicle-mediated transport / mitochondrion organization / GTPase activator activity / SNARE binding / guanyl-nucleotide exchange factor activity / neuron projection morphogenesis / intracellular protein transport / trans-Golgi network / cytoplasmic vesicle membrane / positive regulation of neuron projection development / small GTPase binding / phagocytic vesicle membrane / melanosome / protein transport / late endosome / mitochondrial outer membrane / lysosome / early endosome / neuron projection / intracellular membrane-bounded organelle / GTPase activity / GTP binding / endoplasmic reticulum / mitochondrion / membrane / plasma membrane / cytosol
Similarity search - Function
Ras-related protein Rab29/Rab38/Rab32 / VPS9 domain / VPS9 domain superfamily / Vacuolar sorting protein 9 (VPS9) domain / VPS9 domain profile. / Domain present in VPS9 / small GTPase Rab1 family profile. / Ankyrin repeat-containing domain / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Ankyrin repeat ...Ras-related protein Rab29/Rab38/Rab32 / VPS9 domain / VPS9 domain superfamily / Vacuolar sorting protein 9 (VPS9) domain / VPS9 domain profile. / Domain present in VPS9 / small GTPase Rab1 family profile. / Ankyrin repeat-containing domain / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Ankyrin repeat / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / Ras-related protein Rab-32 / Ankyrin repeat domain-containing protein 27
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsPerez-Dorado, I. / Schaefer, I.B. / McCoy, A.J. / Owen, D.J. / Evans, P.R.
CitationJournal: Dev.Cell / Year: 2014
Title: Varp is Recruited on to Endosomes by Direct Interaction with Retromer, Where Together They Function in Export to the Cell Surface.
Authors: Hesketh, G.G. / Perez-Dorado, I. / Jackson, L.P. / Wartosch, L. / Schefer, I.B. / Gray, S.R. / Mccoy, A.J. / Zeldin, O.B. / Garman, E.F. / Harbour, M.E. / Evans, P.R. / Seaman, M.N. / Luzio, J.P. / Owen, D.J.
History
DepositionApr 13, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 4, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 25, 2014Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.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_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_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_label_seq_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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: RAS-RELATED PROTEIN RAB-32
B: RAS-RELATED PROTEIN RAB-32
C: RAS-RELATED PROTEIN RAB-32
D: ANKYRIN REPEAT DOMAIN-CONTAINING PROTEIN 27
E: ANKYRIN REPEAT DOMAIN-CONTAINING PROTEIN 27
F: ANKYRIN REPEAT DOMAIN-CONTAINING PROTEIN 27
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,85012
Polymers143,2146
Non-polymers1,6376
Water2,360131
1
A: RAS-RELATED PROTEIN RAB-32
D: ANKYRIN REPEAT DOMAIN-CONTAINING PROTEIN 27
hetero molecules

A: RAS-RELATED PROTEIN RAB-32
D: ANKYRIN REPEAT DOMAIN-CONTAINING PROTEIN 27
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,5678
Polymers95,4764
Non-polymers1,0914
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area7100 Å2
ΔGint-35.5 kcal/mol
Surface area34710 Å2
MethodPISA
2
B: RAS-RELATED PROTEIN RAB-32
E: ANKYRIN REPEAT DOMAIN-CONTAINING PROTEIN 27
hetero molecules

C: RAS-RELATED PROTEIN RAB-32
F: ANKYRIN REPEAT DOMAIN-CONTAINING PROTEIN 27
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,5678
Polymers95,4764
Non-polymers1,0914
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_545x-y,-y-1,-z+1/31
Buried area19000 Å2
ΔGint-43.7 kcal/mol
Surface area34450 Å2
MethodPISA
3
C: RAS-RELATED PROTEIN RAB-32
F: ANKYRIN REPEAT DOMAIN-CONTAINING PROTEIN 27
hetero molecules

B: RAS-RELATED PROTEIN RAB-32
E: ANKYRIN REPEAT DOMAIN-CONTAINING PROTEIN 27
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,5678
Polymers95,4764
Non-polymers1,0914
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_445x-y-1,-y-1,-z+1/31
Buried area19000 Å2
ΔGint-43.7 kcal/mol
Surface area34450 Å2
MethodPISA
4
A: RAS-RELATED PROTEIN RAB-32
D: ANKYRIN REPEAT DOMAIN-CONTAINING PROTEIN 27
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2834
Polymers47,7382
Non-polymers5462
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1700 Å2
ΔGint-6.8 kcal/mol
Surface area19210 Å2
MethodPISA
5
B: RAS-RELATED PROTEIN RAB-32
E: ANKYRIN REPEAT DOMAIN-CONTAINING PROTEIN 27
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2834
Polymers47,7382
Non-polymers5462
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1750 Å2
ΔGint-8.6 kcal/mol
Surface area18640 Å2
MethodPISA
6
C: RAS-RELATED PROTEIN RAB-32
F: ANKYRIN REPEAT DOMAIN-CONTAINING PROTEIN 27
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2834
Polymers47,7382
Non-polymers5462
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1630 Å2
ΔGint-7.8 kcal/mol
Surface area19070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)144.445, 144.445, 135.680
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C
14D
24E
15D
25F
16E
26F

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLUHISHISAA23 - 19628 - 201
21GLUGLUHISHISBB23 - 19628 - 201
12ARGARGSERSERAA22 - 19827 - 203
22ARGARGSERSERCC22 - 19827 - 203
13GLUGLUHISHISBB23 - 19628 - 201
23GLUGLUHISHISCC23 - 19628 - 201
14VALVALALAALADD453 - 61610 - 173
24VALVALALAALAEE453 - 61610 - 173
15VALVALTYRTYRDD453 - 61710 - 174
25VALVALTYRTYRFF453 - 61710 - 174
16VALVALALAALAEE453 - 61610 - 173
26VALVALALAALAFF453 - 61610 - 173

NCS ensembles :
ID
1
2
3
4
5
6

-
Components

#1: Protein RAS-RELATED PROTEIN RAB-32 / RAB32


Mass: 25425.762 Da / Num. of mol.: 3 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGEX-6P-1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA 2 / References: UniProt: Q13637, small monomeric GTPase
#2: Protein ANKYRIN REPEAT DOMAIN-CONTAINING PROTEIN 27 / VPS9-DOMAIN ANKYRIN REPEAT PROTEIN / VPS9 DOMAIN-CONTAINING P


Mass: 22312.137 Da / Num. of mol.: 3
Fragment: FIRST ANKYRIN REPEAT-CONTAINING DOMAIN, RESIDUES 450-640
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGEX-6P-1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA 2 / References: UniProt: Q96NW4
#3: Chemical ChemComp-GCP / PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER


Mass: 521.208 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C11H18N5O13P3 / Comment: GMP-PCP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 131 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsNTERMINAL SEQUENCE GPLGSM IS AN INSERTION COMING FROM THE EXPRESSION PLASMID USED. GLN 85 WAS ...NTERMINAL SEQUENCE GPLGSM IS AN INSERTION COMING FROM THE EXPRESSION PLASMID USED. GLN 85 WAS MUTATED TO LEU NTERMINAL SEQUENCE GPLGSM IS AN INSERTION COMING FROM THE EXPRESSION PLASMID USED. LAST SIX RESIDUES CORRESPONDS TO THE 6HIS-TAG

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

-
Sample preparation

CrystalDensity Matthews: 2.82 Å3/Da / Density % sol: 56.3 % / Description: NONE

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 6, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.8→72.22 Å / Num. obs: 40077 / % possible obs: 98.8 % / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Rmerge(I) obs: 0.24 / Net I/σ(I): 8.8
Reflection shellResolution: 2.8→2.91 Å / Redundancy: 5 % / Rmerge(I) obs: 1.5 / Mean I/σ(I) obs: 0.9 / % possible all: 94.1

-
Processing

Software
NameVersionClassification
REFMAC5.8.0069refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1YHN AND 4B93

1yhn

4b93


Resolution: 2.8→125.09 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.926 / SU B: 16.544 / SU ML: 0.291 / Cross valid method: THROUGHOUT / ESU R: 0.717 / ESU R Free: 0.329 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY MISSING RESIDUES. RESIDUES 1-21 AND 199-225 OF BOTH CHAINS A AND C. RESIDUES 1-22 AND 198-225 OF CHAIN B. ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY MISSING RESIDUES. RESIDUES 1-21 AND 199-225 OF BOTH CHAINS A AND C. RESIDUES 1-22 AND 198-225 OF CHAIN B. RESIDUES 450-451 AND 619-640 OF CHAIN D. RESIDUES 450-452 AND 618- 640 OF CHAIN E. RESIDUES 450-452 AND 619-640 OF CHAIN F. RESIDUES FROM -5 TO 0. CTERMINAL 6HIS TAGS IN CHAINS D, E, AND F.
RfactorNum. reflection% reflectionSelection details
Rfree0.24565 2011 5 %RANDOM
Rwork0.19205 ---
obs0.19466 38004 98.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 74.856 Å2
Baniso -1Baniso -2Baniso -3
1-1.4 Å20.7 Å20 Å2
2--1.4 Å20 Å2
3----4.53 Å2
Refinement stepCycle: LAST / Resolution: 2.8→125.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8052 0 99 131 8282
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0198340
X-RAY DIFFRACTIONr_bond_other_d0.0050.027915
X-RAY DIFFRACTIONr_angle_refined_deg1.5391.95811311
X-RAY DIFFRACTIONr_angle_other_deg1.076318165
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0750.21276
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.029380
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021949
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.2127.2264102
X-RAY DIFFRACTIONr_mcbond_other5.27.2264101
X-RAY DIFFRACTIONr_mcangle_it8.08310.8235117
X-RAY DIFFRACTIONr_mcangle_other8.08310.8245118
X-RAY DIFFRACTIONr_scbond_it5.5227.7924237
X-RAY DIFFRACTIONr_scbond_other5.5227.7944238
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.74911.4666195
X-RAY DIFFRACTIONr_long_range_B_refined11.74373.2737167
X-RAY DIFFRACTIONr_long_range_B_other11.74573.297165
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A103240.1
12B103240.1
21A107110.09
22C107110.09
31B104420.1
32C104420.1
41D93750.1
42E93750.1
51D94150.11
52F94150.11
61E94170.11
62F94170.11
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.437 136 -
Rwork0.38 2628 -
obs--91.61 %

+
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