[English] 日本語
Yorodumi
- PDB-3rl7: Crystal structure of hDLG1-PDZ1 complexed with APC -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3rl7
TitleCrystal structure of hDLG1-PDZ1 complexed with APC
Components
  • 11-mer peptide from Adenomatous polyposis coli protein
  • Disks large homolog 1
KeywordsMEMBRANE PROTEIN/SIGNALING PROTEIN / PDZ-ligand complex / MEMBRANE PROTEIN-SIGNALING PROTEIN complex
Function / homology
Function and homology information


regulation of voltage-gated potassium channel activity involved in ventricular cardiac muscle cell action potential repolarization / regulation of protein localization to synapse / regulation of potassium ion import / L27 domain binding / regulation of potassium ion export across plasma membrane / MPP7-DLG1-LIN7 complex / APC truncation mutants are not K63 polyubiquitinated / membrane raft organization / regulation of microtubule-based movement / hard palate development ...regulation of voltage-gated potassium channel activity involved in ventricular cardiac muscle cell action potential repolarization / regulation of protein localization to synapse / regulation of potassium ion import / L27 domain binding / regulation of potassium ion export across plasma membrane / MPP7-DLG1-LIN7 complex / APC truncation mutants are not K63 polyubiquitinated / membrane raft organization / regulation of microtubule-based movement / hard palate development / negative regulation of cell cycle G1/S phase transition / establishment of centrosome localization / cortical microtubule organization / negative regulation of p38MAPK cascade / guanylate kinase activity / NrCAM interactions / regulation of sodium ion transmembrane transport / embryonic skeletal system morphogenesis / astral microtubule organization / structural constituent of postsynaptic density / lateral loop / reproductive structure development / myelin sheath abaxonal region / immunological synapse formation / gamma-catenin binding / regulation of attachment of spindle microtubules to kinetochore / positive regulation of pseudopodium assembly / peristalsis / Synaptic adhesion-like molecules / cell projection membrane / positive regulation of protein localization to centrosome / smooth muscle tissue development / pattern specification process / bicellular tight junction assembly / protein kinase regulator activity / positive regulation of potassium ion transport / negative regulation of microtubule depolymerization / regulation of ventricular cardiac muscle cell action potential / negative regulation of cyclin-dependent protein serine/threonine kinase activity / amyloid precursor protein metabolic process / node of Ranvier / APC truncation mutants have impaired AXIN binding / AXIN missense mutants destabilize the destruction complex / Truncations of AMER1 destabilize the destruction complex / microtubule plus-end binding / beta-catenin destruction complex / regulation of microtubule-based process / Trafficking of AMPA receptors / establishment or maintenance of epithelial cell apical/basal polarity / heart valve development / protein-containing complex localization / Beta-catenin phosphorylation cascade / Signaling by GSK3beta mutants / CTNNB1 S33 mutants aren't phosphorylated / CTNNB1 S37 mutants aren't phosphorylated / CTNNB1 S45 mutants aren't phosphorylated / CTNNB1 T41 mutants aren't phosphorylated / catenin complex / Assembly and cell surface presentation of NMDA receptors / endothelial cell proliferation / Wnt signalosome / Disassembly of the destruction complex and recruitment of AXIN to the membrane / neurotransmitter receptor localization to postsynaptic specialization membrane / cell fate specification / lens development in camera-type eye / regulation of myelination / Activation of Ca-permeable Kainate Receptor / cortical actin cytoskeleton organization / endocardial cushion morphogenesis / establishment or maintenance of cell polarity / branching involved in ureteric bud morphogenesis / dynein complex binding / negative regulation of G1/S transition of mitotic cell cycle / positive regulation of actin filament polymerization / receptor clustering / mitotic spindle assembly checkpoint signaling / Negative regulation of NMDA receptor-mediated neuronal transmission / Unblocking of NMDA receptors, glutamate binding and activation / Apoptotic cleavage of cellular proteins / regulation of cell differentiation / phosphoprotein phosphatase activity / Long-term potentiation / mitotic cytokinesis / immunological synapse / basement membrane / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / bicellular tight junction / intercalated disc / potassium channel regulator activity / lateral plasma membrane / phosphatase binding / T cell proliferation / negative regulation of T cell proliferation / actin filament polymerization / Ras activation upon Ca2+ influx through NMDA receptor / regulation of membrane potential / cytoskeletal protein binding / phosphatidylinositol 3-kinase/protein kinase B signal transduction / synaptic membrane / actin filament organization
Similarity search - Function
L27-1 / L27_1 / Adenomatous polyposis coli tumour suppressor protein / Armadillo-associated region on APC / Unstructured region on APC between 1st and 2nd catenin-bdg motifs / Unstructured region on APC between 1st two creatine-rich regions / Unstructured region on APC between APC_crr and SAMP / Unstructured region on APC between SAMP and APC_crr / Unstructured region on APC between APC_crr regions 5 and 6 / Adenomatous polyposis coli protein repeat ...L27-1 / L27_1 / Adenomatous polyposis coli tumour suppressor protein / Armadillo-associated region on APC / Unstructured region on APC between 1st and 2nd catenin-bdg motifs / Unstructured region on APC between 1st two creatine-rich regions / Unstructured region on APC between APC_crr and SAMP / Unstructured region on APC between SAMP and APC_crr / Unstructured region on APC between APC_crr regions 5 and 6 / Adenomatous polyposis coli protein repeat / SAMP / EB-1 binding / Adenomatous polyposis coli protein basic domain / Adenomatous polyposis coli protein, 15 residue repeat / Adenomatous polyposis coli (APC) family / Adenomatous polyposis coli protein / Adenomatous polyposis coli, N-terminal dimerisation domain / APC, N-terminal coiled-coil domain superfamily / Adenomatous polyposis coli (APC) repeat / APC repeat / SAMP Motif / EB-1 Binding Domain / APC basic domain / APC 15 residue motif / Coiled-coil N-terminus of APC, dimerisation domain / Adenomatous polyposis coli (APC) repeat / domain in receptor targeting proteins Lin-2 and Lin-7 / L27 domain / L27 domain profile. / Polyubiquitination (PEST) N-terminal domain of MAGUK / L27 domain superfamily / Disks large homologue 1, N-terminal PEST domain / Polyubiquitination (PEST) N-terminal domain of MAGUK / PDZ-associated domain of NMDA receptors / PDZ-associated domain of NMDA receptors / Disks large 1-like / Guanylate kinase, conserved site / Guanylate kinase-like signature. / Guanylate kinase-like domain profile. / Guanylate kinase-like domain / Armadillo/plakoglobin ARM repeat profile. / Guanylate kinase/L-type calcium channel beta subunit / Guanylate kinase / Guanylate kinase homologues. / Armadillo/beta-catenin-like repeat / Armadillo/beta-catenin-like repeats / Armadillo / PDZ domain / Pdz3 Domain / PDZ domain / SH3 domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Armadillo-like helical / Armadillo-type fold / Roll / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Adenomatous polyposis coli protein / Disks large homolog 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsZhang, Z. / Li, H. / Wu, G.
CitationJournal: Plos One / Year: 2011
Title: Molecular basis for the recognition of adenomatous polyposis coli by the Discs Large 1 protein.
Authors: Zhang, Z. / Li, H. / Chen, L. / Lu, X. / Zhang, J. / Xu, P. / Lin, K. / Wu, G.
History
DepositionApr 19, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 14, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2016Group: Structure summary
Revision 1.2Nov 1, 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 / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Disks large homolog 1
A: Disks large homolog 1
C: Disks large homolog 1
D: Disks large homolog 1
E: Disks large homolog 1
F: Disks large homolog 1
G: 11-mer peptide from Adenomatous polyposis coli protein
H: 11-mer peptide from Adenomatous polyposis coli protein
I: 11-mer peptide from Adenomatous polyposis coli protein
J: 11-mer peptide from Adenomatous polyposis coli protein
K: 11-mer peptide from Adenomatous polyposis coli protein
L: 11-mer peptide from Adenomatous polyposis coli protein


Theoretical massNumber of molelcules
Total (without water)78,43612
Polymers78,43612
Non-polymers00
Water1,02757
1
A: Disks large homolog 1
G: 11-mer peptide from Adenomatous polyposis coli protein


Theoretical massNumber of molelcules
Total (without water)13,0732
Polymers13,0732
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Disks large homolog 1
H: 11-mer peptide from Adenomatous polyposis coli protein


Theoretical massNumber of molelcules
Total (without water)13,0732
Polymers13,0732
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Disks large homolog 1
J: 11-mer peptide from Adenomatous polyposis coli protein


Theoretical massNumber of molelcules
Total (without water)13,0732
Polymers13,0732
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Disks large homolog 1
I: 11-mer peptide from Adenomatous polyposis coli protein


Theoretical massNumber of molelcules
Total (without water)13,0732
Polymers13,0732
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Disks large homolog 1
K: 11-mer peptide from Adenomatous polyposis coli protein


Theoretical massNumber of molelcules
Total (without water)13,0732
Polymers13,0732
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Disks large homolog 1
L: 11-mer peptide from Adenomatous polyposis coli protein


Theoretical massNumber of molelcules
Total (without water)13,0732
Polymers13,0732
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.627, 105.627, 50.830
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number143
Space group name H-MP3
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A
31C
41D
51E
61F

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ILE / Beg label comp-ID: ILE / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: 4 / Auth seq-ID: 225 - 309 / Label seq-ID: 15 - 99

Dom-IDAuth asym-IDLabel asym-ID
1BA
2AB
3CC
4DD
5EE
6FF

-
Components

#1: Protein
Disks large homolog 1 / Synapse-associated protein 97 / SAP-97 / SAP97 / hDlg


Mass: 11865.397 Da / Num. of mol.: 6 / Fragment: UNP RESIDUES 220-317
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DLG1 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q12959
#2: Protein/peptide
11-mer peptide from Adenomatous polyposis coli protein / APC-C11


Mass: 1207.338 Da / Num. of mol.: 6 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans / Source: (synth.) Homo sapiens (human) / References: UniProt: P25054
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 57 / 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: 2.09 Å3/Da / Density % sol: 41.07 % / Mosaicity: 1.686 °
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.8M Na2HPO4, 0.9M KH2PO4, pH 7.5, vapor diffusion, hanging drop, temperature 287K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97916 Å
DetectorDetector: CCD / Date: Nov 30, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97916 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.262
11h+k,-k,-l20.239
11-h,-k,l30.261
11K, H, -L40.238
ReflectionResolution: 2.3→50.01 Å / Num. obs: 28225 / % possible obs: 99.9 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.099 / Χ2: 1.002 / Net I/σ(I): 12.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.3-2.384.90.35328121.0041100
2.38-2.484.90.29728141.0011100
2.48-2.594.90.23428351.0061100
2.59-2.735.10.18728561.0091100
2.73-2.95.50.15128121.0031100
2.9-3.125.90.12128071.0011100
3.12-3.446.40.11428380.9991100
3.44-3.936.80.128171.0021100
3.93-4.956.90.07528161.0021100
4.95-506.90.06128181.001199.3

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASERphasing
REFMAC5.5.0102refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ZOK

1zok


Resolution: 2.3→50 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.902 / Occupancy max: 1 / Occupancy min: 1 / SU B: 16.83 / SU ML: 0.164 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.046 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2314 1392 4.9 %RANDOM
Rwork0.1925 ---
obs0.1944 28155 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 106.68 Å2 / Biso mean: 38.498 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1-14.62 Å20 Å20 Å2
2--14.62 Å20 Å2
3----29.25 Å2
Refinement stepCycle: LAST / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4295 0 0 57 4352
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0224318
X-RAY DIFFRACTIONr_angle_refined_deg0.971.9655808
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7115548
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.35123.163196
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.62715759
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7951546
X-RAY DIFFRACTIONr_chiral_restr0.0660.2687
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023189
Refine LS restraints NCS

Ens-ID: 1 / Number: 563 / Refine-ID: X-RAY DIFFRACTION / Type: MEDIUM POSITIONAL / Weight position: 0.5

Dom-IDAuth asym-IDRms dev position (Å)
1B0.49
2A0.5
3C0.47
4D0.42
5E0.44
6F0.4
LS refinement shellResolution: 2.299→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 100 -
Rwork0.231 1936 -
all-2036 -
obs--98.36 %
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)
12.5291-0.4846-0.30162.8960.29081.92340.0299-0.0750.10310.014-0.06050.0742-0.1888-0.17850.03060.02040.0161-0.01160.0221-0.00430.089639.9335-20.6765-4.7908
21.115-0.17680.14772.5338-0.53021.418-0.06540.10980.1254-0.0198-0.00650.1-0.247-0.07060.07190.06250.00240.00670.0198-0.00870.100850.254-14.035217.3585
31.36040.1804-0.74450.9317-0.67541.5987-0.00240.0260.1605-0.1055-0.0355-0.164-0.15450.23080.03790.1208-0.0179-0.02040.0901-0.01010.150812.22710.252417.5968
42.0541-0.16650.28622.0543-0.55081.49550.012-0.0558-0.13310.0905-0.0102-0.13130.03350.1382-0.00180.01740.02450.00660.084-0.02170.116913.4146-9.9981-4.4952
51.20620.65380.00440.3906-0.10690.68760.0782-0.10680.02920.0366-0.05450.0680.1049-0.1981-0.02360.16950.01970.01510.1849-0.0040.222338.703825.0949-5.1159
60.90630.0238-0.17091.81440.24571.4194-0.03840.1449-0.1292-0.0879-0.0072-0.03670.0584-0.01460.04560.0933-0.0191-0.01910.030.00110.170254.796213.916517.1066
70.9684-0.9454-0.18015.25140.97090.1977-0.7099-0.33470.06410.2620.73110.52950.03750.1517-0.02130.51340.1851-0.03240.16460.00320.432349.2039-4.424224.791
845.0916-20.0296-2.245411.70354.7685.1781-0.06460.5250.5925-0.2953-0.28090.0123-0.4323-0.08790.34550.12560.03260.00380.10590.07290.159132.3639-14.9696-13.2771
94.42411.3845-2.70640.4983-0.89811.7010.00930.4637-0.0304-0.13640.0014-0.04840.0996-0.1715-0.01070.32870.2890.06230.3267-0.04350.319821.6409-16.6215-12.6454
103.43036.2029-1.148418.14251.41062.14240.0530.00040.44920.18350.21870.54570.04430.1085-0.27170.1518-0.0255-0.0550.30160.01090.221519.865116.442525.6511
1137.134-3.842916.51570.4031-1.71627.3546-0.4566-0.51651.2392-0.0008-0.0013-0.0933-0.1277-0.22490.45790.46090.0265-0.17610.4134-0.00220.438731.26622.0446-13.1611
122.6724-1.153710.21730.5029-4.395739.12220.186-0.2053-0.0893-0.04350.02390.10491.2237-0.7424-0.20991.14780.11530.81980.12480.06140.950955.12795.384225.3685
130.1761-0.0794-0.02120.0464-0.00040.01310.03350.1115-0.0070.0115-0.0479-0.0047-0.0318-0.00950.01450.08150.0081-0.02450.08320.01330.074631.4371-2.71164.8052
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B219 - 310
2X-RAY DIFFRACTION2A220 - 309
3X-RAY DIFFRACTION3C220 - 310
4X-RAY DIFFRACTION4D219 - 310
5X-RAY DIFFRACTION5E220 - 310
6X-RAY DIFFRACTION6F219 - 309
7X-RAY DIFFRACTION7G2837 - 2843
8X-RAY DIFFRACTION8H2838 - 2842
9X-RAY DIFFRACTION9I2838 - 2842
10X-RAY DIFFRACTION10J2838 - 2843
11X-RAY DIFFRACTION11K2839 - 2843
12X-RAY DIFFRACTION12L2839 - 2842
13X-RAY DIFFRACTION13B1 - 54

+
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