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- PDB-4cym: Complex of human VARP-ANKRD1 with Rab32-GppCp -

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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 / negative regulation of SNARE complex assembly / AP-1 adaptor complex binding / tubular endosome / endosome to melanosome transport / melanosome assembly / phagosome maturation / mitochondria-associated endoplasmic reticulum membrane contact site / early endosome to late endosome transport ...BLOC-2 complex binding / AP-3 adaptor complex binding / negative regulation of SNARE complex assembly / AP-1 adaptor complex binding / tubular endosome / endosome to melanosome transport / melanosome assembly / phagosome maturation / mitochondria-associated endoplasmic reticulum membrane contact site / early endosome to late endosome transport / GTP-dependent protein binding / RAB geranylgeranylation / melanosome membrane / melanosome organization / positive regulation of dendrite morphogenesis / RAB GEFs exchange GTP for GDP on RABs / endocytic recycling / protein localization to membrane / antigen processing and presentation / transport vesicle / phagocytic vesicle / vesicle-mediated transport / neuron projection morphogenesis / endomembrane system / GTPase activator activity / cytoplasmic vesicle membrane / guanyl-nucleotide exchange factor activity / small monomeric GTPase / SNARE binding / mitochondrion organization / intracellular protein transport / trans-Golgi network / positive regulation of neuron projection development / small GTPase binding / phagocytic vesicle membrane / melanosome / late endosome / protein transport / mitochondrial outer membrane / early endosome / lysosome / 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 Rab domain profile. / Ankyrin repeat-containing domain / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases ...: / 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 Rab domain 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 / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Rab subfamily of small GTPases / 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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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: _ / Refine code: _

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

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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


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

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Experimental details

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Experiment

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

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Sample preparation

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

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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

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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 %

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