[English] 日本語
Yorodumi
- PDB-5j89: Structure of human Programmed cell death 1 ligand 1 (PD-L1) with ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5j89
TitleStructure of human Programmed cell death 1 ligand 1 (PD-L1) with low molecular mass inhibitor
ComponentsProgrammed cell death 1 ligand 1
KeywordsIMMUNE SYSTEM / PD-L1 / Programmed cell death 1 ligand 1 / cell cycle
Function / homology
Function and homology information


negative regulation of tumor necrosis factor superfamily cytokine production / positive regulation of activated CD8-positive, alpha-beta T cell apoptotic process / negative regulation of CD8-positive, alpha-beta T cell activation / Regulation of PD-L1(CD274) translation / negative regulation of T cell mediated immune response to tumor cell / negative regulation of CD4-positive, alpha-beta T cell proliferation / TRIF-dependent toll-like receptor signaling pathway / STAT3 nuclear events downstream of ALK signaling / negative regulation of activated T cell proliferation / negative regulation of interleukin-10 production ...negative regulation of tumor necrosis factor superfamily cytokine production / positive regulation of activated CD8-positive, alpha-beta T cell apoptotic process / negative regulation of CD8-positive, alpha-beta T cell activation / Regulation of PD-L1(CD274) translation / negative regulation of T cell mediated immune response to tumor cell / negative regulation of CD4-positive, alpha-beta T cell proliferation / TRIF-dependent toll-like receptor signaling pathway / STAT3 nuclear events downstream of ALK signaling / negative regulation of activated T cell proliferation / negative regulation of interleukin-10 production / negative regulation of T cell activation / negative regulation of type II interferon production / positive regulation of interleukin-10 production / Co-inhibition by PD-1 / negative regulation of T cell receptor signaling pathway / negative regulation of T cell proliferation / T cell costimulation / response to cytokine / positive regulation of T cell proliferation / PD-L1(CD274) glycosylation and translocation to plasma membrane / AMPK-induced ERAD and lysosome mediated degradation of PD-L1(CD274) / GSK3B-mediated proteasomal degradation of PD-L1(CD274) / recycling endosome membrane / SPOP-mediated proteasomal degradation of PD-L1(CD274) / cellular response to lipopolysaccharide / early endosome membrane / adaptive immune response / cell surface receptor signaling pathway / transcription coactivator activity / nuclear speck / immune response / receptor ligand activity / external side of plasma membrane / Golgi membrane / endoplasmic reticulum membrane / signal transduction / extracellular exosome / nucleoplasm / plasma membrane / cytosol
Similarity search - Function
: / CD80-like, immunoglobulin C2-set / CD80-like C2-set immunoglobulin domain / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily ...: / CD80-like, immunoglobulin C2-set / CD80-like C2-set immunoglobulin domain / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Chem-6GX / Programmed cell death 1 ligand 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsZak, K.M. / Grudnik, P. / Guzik, K. / Zieba, B.J. / Musielak, B. / Doemling, P. / Dubin, G. / Holak, T.A.
Funding support Poland, 5items
OrganizationGrant numberCountry
European CommissionaMarie Curie FP7-Reintegration-Grant Poland
National Science CentreUMO-2012/06/A/ST5/00224 Poland
National Science CentreUMO-2011/01/D/NZ1/01169 Poland
European UnionPOIG.02.01.00-12-064/08 Poland
European UnionPOIG.02.01.00-12-167/08 Poland
CitationJournal: Oncotarget / Year: 2016
Title: Structural basis for small molecule targeting of the programmed death ligand 1 (PD-L1).
Authors: Zak, K.M. / Grudnik, P. / Guzik, K. / Zieba, B.J. / Musielak, B. / Domling, A. / Dubin, G. / Holak, T.A.
History
DepositionApr 7, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 27, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 14, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: 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
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
C: Programmed cell death 1 ligand 1
A: Programmed cell death 1 ligand 1
D: Programmed cell death 1 ligand 1
B: Programmed cell death 1 ligand 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,8387
Polymers66,9374
Non-polymers9013
Water3,747208
1
C: Programmed cell death 1 ligand 1
D: Programmed cell death 1 ligand 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8883
Polymers33,4692
Non-polymers4201
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Programmed cell death 1 ligand 1
B: Programmed cell death 1 ligand 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9504
Polymers33,4692
Non-polymers4822
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.834, 85.093, 161.772
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
Programmed cell death 1 ligand 1 / Programmed death ligand 1 / B7 homolog 1 / B7-H1


Mass: 16734.254 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD274, B7H1, PDCD1L1, PDCD1LG1, PDL1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NZQ7
#2: Chemical ChemComp-6GX / N-{2-[({2-methoxy-6-[(2-methyl[1,1'-biphenyl]-3-yl)methoxy]pyridin-3-yl}methyl)amino]ethyl}acetamide


Mass: 419.516 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H29N3O3
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 208 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 41.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.01M Tris pH=8.5, 0.3M sodium chloride, 27% (w/v) PEG 4000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918409 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 21, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918409 Å / Relative weight: 1
ReflectionResolution: 2.2→42.55 Å / Num. obs: 29405 / % possible obs: 99.3 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 23
Reflection shellResolution: 2.2→2.279 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.272 / Mean I/σ(I) obs: 6.3 / % possible all: 99

-
Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5C3T

5c3t


Resolution: 2.2→42.547 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.61
RfactorNum. reflection% reflection
Rfree0.256 1490 5.07 %
Rwork0.2023 --
obs0.2051 29405 99.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.2→42.547 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3827 0 66 208 4101
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084004
X-RAY DIFFRACTIONf_angle_d1.0055450
X-RAY DIFFRACTIONf_dihedral_angle_d18.612357
X-RAY DIFFRACTIONf_chiral_restr0.06613
X-RAY DIFFRACTIONf_plane_restr0.006694
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2001-2.27110.32581160.26232500X-RAY DIFFRACTION99
2.2711-2.35220.30891320.24562481X-RAY DIFFRACTION100
2.3522-2.44640.35071210.23682499X-RAY DIFFRACTION99
2.4464-2.55770.30681390.24312511X-RAY DIFFRACTION99
2.5577-2.69260.30871360.24132481X-RAY DIFFRACTION100
2.6926-2.86120.29031320.23142522X-RAY DIFFRACTION100
2.8612-3.08210.26551370.23772510X-RAY DIFFRACTION100
3.0821-3.39210.271470.22222560X-RAY DIFFRACTION100
3.3921-3.88270.28231350.19652535X-RAY DIFFRACTION100
3.8827-4.89070.20431420.15182601X-RAY DIFFRACTION100
4.8907-42.55440.19441530.17222715X-RAY DIFFRACTION99
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)
11.7069-1.46560.64164.9322-2.93156.0591-0.2148-0.54020.34510.0861-0.1071-0.7068-0.3030.07920.22790.1558-0.0196-0.07280.3528-0.08480.365415.700529.0107196.4752
21.0846-0.3756-0.0275.4175-0.51941.5779-0.075-0.0354-0.2185-0.05150.18641.00750.0889-0.0447-0.08890.13940.0478-0.01990.25630.03610.38195.698725.6882195.475
31.42810.04790.50640.0598-0.22691.2240.309-0.0596-0.6703-0.2383-0.01370.34840.429-0.3604-0.10430.3668-0.0294-0.34790.61220.12970.61020.4826.6543186.8634
40.82360.7574-0.14415.36371.67063.8090.4828-0.2601-0.0042-1.09070.4453-0.6486-0.3723-0.9873-0.65380.54360.0082-0.11110.6378-0.00310.9616-3.666428.4794185.5154
52.5631.4287-0.85640.892-0.54990.3395-0.61470.8070.0012-0.60440.59030.5080.0912-0.29350.73650.5432-0.255-0.18490.5787-0.12381.5631-4.744617.1002190.3477
62.53271.28860.7741.95050.4630.9172-0.10020.1889-0.32870.5429-0.26231.11620.1535-0.28450.26740.23140.0350.10760.2853-0.04670.6221.289529.7218198.7586
71.32131.02620.6644.61781.04830.39990.0144-0.013-0.0245-0.70990.16321.21930.0422-0.1946-0.15270.1223-0.0745-0.07980.3210.00780.42915.796721.754191.9601
82.27543.0829-2.05625.8778-4.64784.5448-0.18210.3327-0.235-0.37060.35150.23630.17990.1781-0.10330.13050.0104-0.03190.2243-0.05480.26911.956218.8612193.9116
96.7533-0.93690.44115.7261-2.49036.88330.34760.65620.3531-0.6359-0.09451.77420.1582-0.3472-0.32280.2272-0.0105-0.0960.34020.09460.6514-0.4528-0.772195.173
101.3648-0.4125-0.51945.85931.20612.6636-0.010.0834-0.09990.61340.09870.69840.8182-0.2192-0.15280.2441-0.0036-0.04570.19050.06870.31348.5561-10.5499196.1034
112.63760.15981.23143.13561.01113.0616-0.086-0.0875-0.35030.242-0.03890.56510.5159-0.25330.0970.4305-0.0375-0.03070.20060.03710.332611.9771-22.5162194.2805
123.8304-2.4703-0.37136.21111.52512.54810.74710.47310.3417-1.2804-0.5887-0.2618-0.54270.5364-0.29880.435-0.01550.07510.3521-0.06610.187519.5833-15.9985188.5409
134.5429-3.1028-1.32384.69841.20591.80610.3453-0.3390.6072-0.7593-0.4197-1.0668-0.20130.7026-0.65120.13240.04270.45190.5335-0.11290.636223.6317-14.4459190.5728
141.5053-0.5482-0.51272.1395-0.7850.86710.1998-0.348-0.1096-1.3407-0.0486-1.22540.0340.522-0.27120.6916-0.0396-0.13220.4624-0.04341.017126.7304-12.3613194.025
151.2604-0.3094-1.04592.5665-2.57924.096-0.4019-0.419-0.20710.81240.371-0.87790.41260.3858-0.2040.33920.0851-0.09170.2933-0.07740.360818.6114-19.527200.624
161.481-1.10840.26827.5876-0.06581.6347-0.07120.05310.0713-0.34630.3212-0.35260.27430.1212-0.24130.263-0.0393-0.01730.2431-0.02350.182715.6539-13.1124194.3648
171.72030.0274-0.25046.70537.04358.4714-0.11270.2778-0.0745-0.48480.20880.46490.4888-0.0627-0.09130.3731-0.0281-0.07650.20040.02130.25429.8708-8.5822190.0209
184.50421.68660.5574.9116-0.20043.3837-0.01820.0411-0.24870.21420.2329-0.60980.13480.3777-0.22930.19140.0275-0.06790.2366-0.04750.280718.996910.7024201.439
191.2524-0.7570.24594.84852.053.5559-0.12470.10160.1336-0.5057-0.25020.3988-0.7799-0.6660.23280.30810.1593-0.16880.68910.03920.16186.650728.8745170.7233
202.5679-1.765-1.173.9791.16662.8997-0.1512-0.41450.2322-0.58840.2539-0.1832-0.3984-0.0063-0.02040.2616-0.0467-0.04580.3731-0.00010.207916.714727.8031167.3275
214.21340.3076-0.69816.00371.462.4109-0.592-0.77660.47970.7867-0.0059-0.00670.36510.76610.4660.46420.2085-0.08420.5198-0.10450.283817.201932.4538178.5944
221.4102-0.5744-0.09162.1882.83113.9864-0.3454-0.7898-0.08180.85040.8182-0.10851.08250.7444-0.14670.44850.2423-0.12740.8376-0.06810.241721.107227.8136180.6224
233.5463-1.6097-0.81122.0027-0.60120.8911-0.5891-0.6621.27821.00651.4044-0.88440.19931.17640.31370.45360.3819-0.23950.9374-0.34250.801727.372228.5626178.8141
245.022-2.33050.57866.4082-0.33924.5922-0.3699-0.27151.0162-0.46330.3867-1.0894-0.44150.32720.06110.3348-0.0579-0.04190.4004-0.07670.45820.683636.0874168.3842
252.4499-0.9441-0.61254.06660.45513.0535-0.3988-0.43850.1528-0.12480.3509-0.22040.03060.32990.06550.22110.0965-0.03690.4188-0.00630.179918.813925.2044173.0851
266.0795-4.5411-5.36863.87255.03617.4368-0.4278-0.433-0.2311-0.23920.28310.25290.1215-0.22290.35450.22620.0463-0.00160.4053-0.00290.239312.35620.6839173.0672
270.92862.30510.72527.03561.99460.59550.3249-0.5024-1.2547-0.19930.1239-1.87740.57350.2744-0.01590.32990.16440.06910.64740.18690.660729.21574.3307169.78
280.40460.76180.00214.8215-1.23150.6196-0.34150.1461-0.2683-1.38110.1778-0.89020.81980.36060.05630.80480.22090.20730.43650.02660.460423.1977-7.4957167.1996
291.88871.0127-1.01012.650.85731.8879-0.3214-0.13930.0751-0.48870.0178-0.19941.10090.16870.13541.23440.360.34920.40980.04210.614925.4186-24.6228170.4229
303.2757-1.43810.11946.73730.77032.3091-0.4507-0.1933-0.6288-0.49340.60120.69371.0605-0.32370.05541.11310.0870.09320.54620.06950.402713.0158-16.2048173.4267
312.4766-1.7327-0.41544.95180.54561.0136-0.2740.1215-0.7815-1.3712-0.03350.79750.57620.09780.08751.15230.0449-0.08040.4820.0040.476411.1679-16.3994166.4146
320.40820.8428-0.38621.8627-0.4081.5779-0.27120.5555-0.1999-1.0585-0.1454-0.02041.14090.2564-1.52521.43310.12610.20440.5080.09710.212216.6613-10.2669163.056
332.0569-1.1545-0.36426.3936-1.85781.1127-0.3346-0.26860.014-0.55120.421-0.15910.8949-0.3168-0.24380.85480.12410.14330.4337-0.01070.235317.4759-10.9228173.6626
340.7171-1.22240.40075.1812-4.1514.0598-0.0695-0.10290.1599-0.39370.0343-0.65260.38090.51820.15920.56920.13840.12290.424-0.04590.377621.9439-6.2742173.8299
352.0623-0.64192.44456.29270.26263.08020.1322-1.2465-0.05550.8651-0.62672.12530.4875-0.60360.38980.4455-0.08970.22170.4686-0.14930.47599.103411.2742163.0771
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'C' and (resid 18 through 26 )
2X-RAY DIFFRACTION2chain 'C' and (resid 27 through 61 )
3X-RAY DIFFRACTION3chain 'C' and (resid 62 through 68 )
4X-RAY DIFFRACTION4chain 'C' and (resid 69 through 78 )
5X-RAY DIFFRACTION5chain 'C' and (resid 79 through 84 )
6X-RAY DIFFRACTION6chain 'C' and (resid 85 through 101 )
7X-RAY DIFFRACTION7chain 'C' and (resid 102 through 120 )
8X-RAY DIFFRACTION8chain 'C' and (resid 121 through 131 )
9X-RAY DIFFRACTION9chain 'C' and (resid 132 through 142 )
10X-RAY DIFFRACTION10chain 'A' and (resid 18 through 35 )
11X-RAY DIFFRACTION11chain 'A' and (resid 36 through 49 )
12X-RAY DIFFRACTION12chain 'A' and (resid 50 through 61 )
13X-RAY DIFFRACTION13chain 'A' and (resid 62 through 68 )
14X-RAY DIFFRACTION14chain 'A' and (resid 69 through 84 )
15X-RAY DIFFRACTION15chain 'A' and (resid 85 through 91 )
16X-RAY DIFFRACTION16chain 'A' and (resid 92 through 120 )
17X-RAY DIFFRACTION17chain 'A' and (resid 121 through 131 )
18X-RAY DIFFRACTION18chain 'A' and (resid 132 through 144 )
19X-RAY DIFFRACTION19chain 'D' and (resid 18 through 26 )
20X-RAY DIFFRACTION20chain 'D' and (resid 27 through 49 )
21X-RAY DIFFRACTION21chain 'D' and (resid 50 through 59 )
22X-RAY DIFFRACTION22chain 'D' and (resid 60 through 68 )
23X-RAY DIFFRACTION23chain 'D' and (resid 69 through 84 )
24X-RAY DIFFRACTION24chain 'D' and (resid 85 through 94 )
25X-RAY DIFFRACTION25chain 'D' and (resid 95 through 120 )
26X-RAY DIFFRACTION26chain 'D' and (resid 121 through 131 )
27X-RAY DIFFRACTION27chain 'D' and (resid 132 through 141 )
28X-RAY DIFFRACTION28chain 'B' and (resid 18 through 38 )
29X-RAY DIFFRACTION29chain 'B' and (resid 39 through 49 )
30X-RAY DIFFRACTION30chain 'B' and (resid 50 through 68 )
31X-RAY DIFFRACTION31chain 'B' and (resid 69 through 94 )
32X-RAY DIFFRACTION32chain 'B' and (resid 95 through 105 )
33X-RAY DIFFRACTION33chain 'B' and (resid 106 through 120 )
34X-RAY DIFFRACTION34chain 'B' and (resid 121 through 131 )
35X-RAY DIFFRACTION35chain 'B' and (resid 132 through 142 )

+
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