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- PDB-3rk2: Truncated SNARE complex -

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Basic information

Entry
Database: PDB / ID: 3rk2
TitleTruncated SNARE complex
Components
  • (Synaptosomal-associated protein ...) x 2
  • Syntaxin-1A
  • Vesicle-associated membrane protein 2
KeywordsMEMBRANE PROTEIN/EXOCYTOSIS / SNARE proteins / membrane fusion / MEMBRANE PROTEIN-EXOCYTOSIS complex
Function / homology
Function and homology information


Toxicity of botulinum toxin type C (botC) / Toxicity of tetanus toxin (tetX) / neurotransmitter uptake / Toxicity of botulinum toxin type G (botG) / clathrin-sculpted glutamate transport vesicle membrane / regulation of delayed rectifier potassium channel activity / Toxicity of botulinum toxin type F (botF) / myosin head/neck binding / Toxicity of botulinum toxin type D (botD) / trans-Golgi Network Vesicle Budding ...Toxicity of botulinum toxin type C (botC) / Toxicity of tetanus toxin (tetX) / neurotransmitter uptake / Toxicity of botulinum toxin type G (botG) / clathrin-sculpted glutamate transport vesicle membrane / regulation of delayed rectifier potassium channel activity / Toxicity of botulinum toxin type F (botF) / myosin head/neck binding / Toxicity of botulinum toxin type D (botD) / trans-Golgi Network Vesicle Budding / Toxicity of botulinum toxin type E (botE) / exocytic insertion of neurotransmitter receptor to postsynaptic membrane / Other interleukin signaling / extrinsic component of presynaptic membrane / Acetylcholine Neurotransmitter Release Cycle / synaptobrevin 2-SNAP-25-syntaxin-1a-complexin II complex / synaptobrevin 2-SNAP-25-syntaxin-1a complex / Toxicity of botulinum toxin type A (botA) / synaptobrevin 2-SNAP-25-syntaxin-1a-complexin I complex / Toxicity of botulinum toxin type B (botB) / synaptic vesicle fusion to presynaptic active zone membrane / regulation of synaptic vesicle priming / clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane / Glutamate Neurotransmitter Release Cycle / positive regulation of norepinephrine secretion / Norepinephrine Neurotransmitter Release Cycle / Acetylcholine Neurotransmitter Release Cycle / positive regulation of catecholamine secretion / zymogen granule membrane / clathrin-sculpted monoamine transport vesicle membrane / Serotonin Neurotransmitter Release Cycle / GABA synthesis, release, reuptake and degradation / Dopamine Neurotransmitter Release Cycle / regulated exocytosis / Serotonin Neurotransmitter Release Cycle / GABA synthesis, release, reuptake and degradation / presynaptic dense core vesicle exocytosis / ribbon synapse / synaptic vesicle docking / response to gravity / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / Dopamine Neurotransmitter Release Cycle / Norepinephrine Neurotransmitter Release Cycle / eosinophil degranulation / vesicle fusion / vesicle docking / positive regulation of calcium ion-dependent exocytosis / chloride channel inhibitor activity / secretion by cell / SNARE complex / SNAP receptor activity / Glutamate Neurotransmitter Release Cycle / regulation of vesicle-mediated transport / LGI-ADAM interactions / hormone secretion / calcium-ion regulated exocytosis / actomyosin / positive regulation of intracellular protein transport / Golgi to plasma membrane protein transport / regulation of exocytosis / neurotransmitter receptor internalization / protein localization to membrane / ATP-dependent protein binding / neuron projection terminus / neurotransmitter transport / Sensory processing of sound by inner hair cells of the cochlea / insulin secretion / syntaxin-1 binding / SNARE complex assembly / positive regulation of neurotransmitter secretion / syntaxin binding / clathrin-coated vesicle / synaptic vesicle priming / Lysosome Vesicle Biogenesis / regulation of synapse assembly / regulation of neuron projection development / endosomal transport / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / Other interleukin signaling / Golgi Associated Vesicle Biogenesis / myosin binding / Insulin processing / exocytosis / voltage-gated potassium channel activity / synaptic vesicle exocytosis / positive regulation of exocytosis / modulation of excitatory postsynaptic potential / associative learning / regulation of insulin secretion / positive regulation of excitatory postsynaptic potential / tertiary granule membrane / protein sumoylation / synaptic vesicle endocytosis / calcium channel inhibitor activity / endomembrane system / long-term memory / specific granule membrane / axonal growth cone / response to glucose / presynaptic active zone membrane
Similarity search - Function
Synaptobrevin/Vesicle-associated membrane protein / Synaptosomal-associated protein 25 / SNAP-25 domain / SNAP-25 family / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #110 / Synaptobrevin signature. / Syntaxin / Syntaxin N-terminal domain / Syntaxin, N-terminal domain / Syntaxin ...Synaptobrevin/Vesicle-associated membrane protein / Synaptosomal-associated protein 25 / SNAP-25 domain / SNAP-25 family / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #110 / Synaptobrevin signature. / Syntaxin / Syntaxin N-terminal domain / Syntaxin, N-terminal domain / Syntaxin / SNARE domain / Synaptobrevin-like / Syntaxin/epimorphin, conserved site / Synaptobrevin / Syntaxin / epimorphin family signature. / v-SNARE, coiled-coil homology domain / v-SNARE coiled-coil homology domain profile. / SNARE / Helical region found in SNAREs / t-SNARE coiled-coil homology domain profile. / Target SNARE coiled-coil homology domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Syntaxin-1A / Synaptosomal-associated protein 25 / Vesicle-associated membrane protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Rattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsKuemmel, D. / Reinisch, K.M.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2011
Title: Complexin cross-links prefusion SNAREs into a zigzag array.
Authors: Kummel, D. / Krishnakumar, S.S. / Radoff, D.T. / Li, F. / Giraudo, C.G. / Pincet, F. / Rothman, J.E. / Reinisch, K.M.
History
DepositionApr 17, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 27, 2011Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2011Group: Database references
Revision 1.2Sep 13, 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 / struct_ref_seq_dif / struct_site
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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _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_label_seq_id / _struct_ref_seq_dif.details / _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

Downloads & links

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Assembly

Deposited unit
A: Vesicle-associated membrane protein 2
B: Syntaxin-1A
C: Synaptosomal-associated protein 25
D: Synaptosomal-associated protein 25
E: Vesicle-associated membrane protein 2
F: Syntaxin-1A
G: Synaptosomal-associated protein 25
H: Synaptosomal-associated protein 25
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,62912
Polymers57,4688
Non-polymers1604
Water66737
1
A: Vesicle-associated membrane protein 2
B: Syntaxin-1A
C: Synaptosomal-associated protein 25
D: Synaptosomal-associated protein 25
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8958
Polymers28,7344
Non-polymers1604
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9750 Å2
ΔGint-94 kcal/mol
Surface area13810 Å2
MethodPISA
2
E: Vesicle-associated membrane protein 2
F: Syntaxin-1A
G: Synaptosomal-associated protein 25
H: Synaptosomal-associated protein 25


Theoretical massNumber of molelcules
Total (without water)28,7344
Polymers28,7344
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9740 Å2
ΔGint-95 kcal/mol
Surface area14050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)27.627, 39.769, 102.275
Angle α, β, γ (deg.)83.38, 89.94, 89.87
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21E
12B
22F
13C
23G
14D
24H

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1112A29 - 60
2112E29 - 60
1122B190 - 248
2122F190 - 248
1132C11 - 79
2132G11 - 79
1142D139 - 203
2142H139 - 203

NCS ensembles :
ID
1
2
3
4

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Components

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Synaptosomal-associated protein ... , 2 types, 4 molecules CGDH

#3: Protein Synaptosomal-associated protein 25 / SNAP-25 / Super protein / SUP / Synaptosomal-associated 25 kDa protein


Mass: 9500.615 Da / Num. of mol.: 2 / Fragment: UNP residues 7-82
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SNAP25, SNAP / Production host: Escherichia coli (E. coli) / References: UniProt: P60880
#4: Protein Synaptosomal-associated protein 25 / SNAP-25 / Super protein / SUP / Synaptosomal-associated 25 kDa protein


Mass: 7427.250 Da / Num. of mol.: 2 / Fragment: UNP residues 141-203
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SNAP25, SNAP / Production host: Escherichia coli (E. coli) / References: UniProt: P60880

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Protein/peptide / Protein , 2 types, 4 molecules AEBF

#1: Protein/peptide Vesicle-associated membrane protein 2 / VAMP-2 / Synaptobrevin-2


Mass: 4254.826 Da / Num. of mol.: 2 / Fragment: UNP residues 28-60
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VAMP2, SYB2 / Production host: Escherichia coli (E. coli) / References: UniProt: P63027
#2: Protein Syntaxin-1A / Neuron-specific antigen HPC-1 / Synaptotagmin-associated 35 kDa protein / P35A


Mass: 7551.502 Da / Num. of mol.: 2 / Fragment: UNP residues 191-253
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Stx1a, Sap / Production host: Escherichia coli (E. coli) / References: UniProt: P32851

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Non-polymers , 2 types, 41 molecules

#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 1.94 Å3/Da / Density % sol: 36.67 %
Crystal growTemperature: 294 K / Method: vapor diffusion / pH: 6.5
Details: 0.05 M calcium acetate, 27% 2-methyl-2,4-pentanediol (MPD), 0.1 M sodium cacodylate pH 6.5-7.0, VAPOR DIFFUSION, temperature 294K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9797 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 16, 2010
RadiationMonochromator: double crystal monochrometer / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 21986 / Num. obs: 20205 / % possible obs: 91.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3
Reflection shellResolution: 2.2→2.28 Å / % possible all: 76.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1KIL

1kil


Resolution: 2.2→39.5 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.922 / SU B: 19.529 / SU ML: 0.222 / Cross valid method: THROUGHOUT / ESU R: 0.432 / ESU R Free: 0.261 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.268 1078 5.1 %RANDOM
Rwork0.227 ---
obs0.23 20117 96.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 56.89 Å2
Baniso -1Baniso -2Baniso -3
1-6.03 Å20.45 Å2-0.47 Å2
2---0.88 Å21.54 Å2
3----5.5 Å2
Refinement stepCycle: LAST / Resolution: 2.2→39.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3760 0 4 37 3801
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0213687
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5821.9644951
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.095464
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.81226.143210
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.18215737
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0641532
X-RAY DIFFRACTIONr_chiral_restr0.1140.2565
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022788
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.7891.52312
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.42123694
X-RAY DIFFRACTIONr_scbond_it2.83431375
X-RAY DIFFRACTIONr_scangle_it4.5024.51253
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A119tight positional0.080.05
2B232tight positional0.030.05
3C271tight positional0.030.05
4D261tight positional0.070.05
1A112medium positional0.440.5
2B215medium positional0.040.5
3C267medium positional0.040.5
4D248medium positional0.20.5
1A119tight thermal0.530.5
2B232tight thermal0.210.5
3C271tight thermal0.150.5
4D261tight thermal0.80.5
1A112medium thermal0.712
2B215medium thermal0.222
3C267medium thermal0.32
4D248medium thermal1.032
LS refinement shellResolution: 2.2→2.26 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 76 -
Rwork0.294 1333 -
obs--89.97 %
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)
17.79662.070110.96090.71864.283740.3430.06960.0602-0.0420.09360.12830.031-1.6023-0.2544-0.19790.56020.1543-0.0240.20650.07620.2971-2.4761-10.7158-6.3169
22.7689-1.054-1.01519.2195.724421.40820.0684-0.3231-0.2855-0.3669-0.67570.3450.3943-1.99360.60730.06030.0232-0.0120.41560.03570.416-9.7167-18.0096-26.868
32.03570.6651-2.82863.86069.140337.66150.3450.16090.21490.12880.2782-0.0972-0.8311-0.4788-0.62320.1220.0863-0.03840.17580.04050.2502-5.4504-17.13212.8745
41.2083-0.4142-3.27580.26562.54631.5-0.1754-0.164-0.3125-0.0222-0.02950.07821.1679-0.04130.20490.60120.01720.00840.20120.00250.3415-3.4258-28.8226-38.4173
51.5601-0.4962-5.93811.01042.337928.9344-0.0697-0.12040.0980.2695-0.0018-0.11710.44860.52510.07150.13560.0359-0.08530.10830.0450.2161-1.1132-23.07756.7328
62.6653-16.76030.6282-1.600923.46660.04820.3148-0.0439-0.13780.0160.007-0.15311.0932-0.06420.1169-0.0152-0.01230.19450.01080.2015-0.6566-20.9135-50.0189
71.6918-0.67425.18651.6447-5.135927.8809-0.05210.08180.12420.0684-0.1981-0.2223-0.21860.64950.25020.06690.0243-0.05010.15620.05470.21125.4197-16.6524-5.3456
85.52122.774612.6672.66597.474836.18770.0716-0.178-0.4489-0.28690.15540.1104-0.3815-0.5282-0.2270.1239-0.0085-0.09070.13870.04630.2366-9.2181-18.6954-49.9157
96.5022-2.9633-11.58521.37194.94332.10840.19560.05930.0474-0.18880.0038-0.0070.6915-0.2159-0.19940.6-0.08720.03340.19580.04660.30511.8549-45.68270.1852
106.40921.02890.581812.65167.474730.1029-0.1790.20950.35680.136-0.73980.765-0.1059-1.79020.91880.01750.019-0.04560.3724-0.01040.41474.1144-37.735122.184
111.7393-0.26020.33222.52964.838726.2691-0.0018-0.0574-0.1333-0.22010.0273-0.04450.5663-0.5859-0.02550.1124-0.06090.02110.10970.07520.22978.275-37.971-6.2387
122.3964-0.17992.39460.10540.820724.768-0.26490.15080.42250.0835-0.09380.047-1.523-0.43590.35870.597-0.03020.04830.1444-0.02920.348510.3752-26.677435.0653
131.18780.41614.38221.16971.934425.318-0.07680.1224-0.1095-0.32440.0345-0.0905-0.76870.2270.04220.14720.00910.05380.12910.04920.187712.52-32.4103-12.1321
141.9580.9405-7.47191.3624-2.461434.96130.0739-0.3002-0.03090.2617-0.08340.0356-0.00891.11270.00950.0745-0.0199-0.0310.14170.02060.186613.2973-34.638244.7935
152.04341.3739-6.52831.1184-5.602329.7004-0.2287-0.106-0.1593-0.1969-0.1127-0.16441.0090.49430.34130.13480.05280.02050.13740.06490.244219.347-38.92250.5489
163.1306-1.431-8.29193.21975.39325.2369-0.02650.18690.1990.2219-0.08370.32150.0398-0.48250.11030.06180.0070.00640.12570.01880.21834.4469-36.731545.2879
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A31 - 46
2X-RAY DIFFRACTION2A47 - 60
3X-RAY DIFFRACTION3B190 - 216
4X-RAY DIFFRACTION4B217 - 248
5X-RAY DIFFRACTION5C7 - 47
6X-RAY DIFFRACTION6C48 - 83
7X-RAY DIFFRACTION7D139 - 171
8X-RAY DIFFRACTION8D172 - 203
9X-RAY DIFFRACTION9E29 - 46
10X-RAY DIFFRACTION10E47 - 60
11X-RAY DIFFRACTION11F190 - 218
12X-RAY DIFFRACTION12F219 - 248
13X-RAY DIFFRACTION13G7 - 46
14X-RAY DIFFRACTION14G47 - 83
15X-RAY DIFFRACTION15H139 - 171
16X-RAY DIFFRACTION16H172 - 203

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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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