[English] 日本語
Yorodumi
- PDB-7s59: Crystal structure of the tick evasin EVA-P974 complexed to a chim... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7s59
TitleCrystal structure of the tick evasin EVA-P974 complexed to a chimera made of human chemokines CCL7 and CCL8
Components
  • Evasin P974
  • chimera protein of C-C motif chemokine 7 and C-C motif chemokine 8,C-C motif chemokine 7
KeywordsIMMUNE SYSTEM / Inflammation / Evasin / Chemokine binder / Evasin-chemokine complex
Function / homology
Function and homology information


CCR2 chemokine receptor binding / CCR1 chemokine receptor binding / positive regulation of natural killer cell chemotaxis / negative regulation of leukocyte proliferation / host-mediated suppression of viral genome replication / CCR chemokine receptor binding / chemokine-mediated signaling pathway / eosinophil chemotaxis / C-C chemokine binding / chemokine activity ...CCR2 chemokine receptor binding / CCR1 chemokine receptor binding / positive regulation of natural killer cell chemotaxis / negative regulation of leukocyte proliferation / host-mediated suppression of viral genome replication / CCR chemokine receptor binding / chemokine-mediated signaling pathway / eosinophil chemotaxis / C-C chemokine binding / chemokine activity / positive regulation of leukocyte migration / Chemokine receptors bind chemokines / positive regulation of myoblast fusion / phospholipase activator activity / exocytosis / monocyte chemotaxis / cellular response to ethanol / positive regulation of myoblast differentiation / cytoskeleton organization / response to gamma radiation / response to virus / intracellular calcium ion homeostasis / chemotaxis / antimicrobial humoral immune response mediated by antimicrobial peptide / calcium ion transport / cell-cell signaling / regulation of cell shape / heparin binding / protein kinase activity / positive regulation of cell migration / inflammatory response / signal transduction / extracellular space / extracellular region
Similarity search - Function
Evasins Class A / Evasins Class A / CC chemokine, conserved site / Small cytokines (intercrine/chemokine) C-C subfamily signature. / Chemokine beta/gamma/delta / Intercrine alpha family (small cytokine C-X-C) (chemokine CXC). / Chemokine interleukin-8-like domain / Chemokine interleukin-8-like superfamily / Small cytokines (intecrine/chemokine), interleukin-8 like
Similarity search - Domain/homology
Evasin P974 / C-C motif chemokine 8 / C-C motif chemokine 7
Similarity search - Component
Biological speciesAmblyomma cajennense (Cayenne tick)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.39 Å
AuthorsBhusal, R.P. / Devkota, S.R. / Aryal, P. / Wilce, M.C.J. / Stone, M.J.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia) Australia
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2022
Title: Structure-guided engineering of tick evasins for targeting chemokines in inflammatory diseases.
Authors: Bhusal, R.P. / Aryal, P. / Devkota, S.R. / Pokhrel, R. / Gunzburg, M.J. / Foster, S.R. / Lim, H.D. / Payne, R.J. / Wilce, M.C.J. / Stone, M.J.
History
DepositionSep 10, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
1: Evasin P974
3: Evasin P974
4: chimera protein of C-C motif chemokine 7 and C-C motif chemokine 8,C-C motif chemokine 7
2: chimera protein of C-C motif chemokine 7 and C-C motif chemokine 8,C-C motif chemokine 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4096
Polymers37,2174
Non-polymers1922
Water1629
1
1: Evasin P974
2: chimera protein of C-C motif chemokine 7 and C-C motif chemokine 8,C-C motif chemokine 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7053
Polymers18,6092
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
3: Evasin P974
4: chimera protein of C-C motif chemokine 7 and C-C motif chemokine 8,C-C motif chemokine 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7053
Polymers18,6092
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)126.240, 62.718, 53.966
Angle α, β, γ (deg.)90.000, 93.933, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
111-201-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "1" and ((resid 3 and (name N or name...
d_2ens_1(chain "3" and (resid 3 through 74 or (resid 75...
d_1ens_2(chain "2" and (resid 6 through 23 or (resid 24...
d_2ens_2(chain "4" and (resid 6 through 18 or (resid 19...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1ASPASNA1 - 83
d_21ens_1ASPASNB2 - 84
d_11ens_2SERASPD6 - 68
d_21ens_2SERASPC1 - 63

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(0.843509809317, 0.528644147952, 0.0950082439671), (0.52297184824, -0.84867279638, 0.0790881194219), (0.122440383592, -0.0170249675873, -0.992329835763)15.1813088807, -3.86262324605, 47.0628960059
2given(0.862217296331, 0.493038770503, 0.116164128232), (0.487070711541, -0.869950840118, 0.0771210589675), (0.139080753041, -0.00991496635946, -0.990231406074)14.8093519999, -3.35121143455, 46.5688960808

-
Components

#1: Protein Evasin P974


Mass: 9702.080 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Amblyomma cajennense (Cayenne tick) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A023FDY8
#2: Protein chimera protein of C-C motif chemokine 7 and C-C motif chemokine 8,C-C motif chemokine 7 / HC14 / Monocyte chemoattractant protein 2 / Monocyte chemotactic protein 2 / MCP-2 / Small- ...HC14 / Monocyte chemoattractant protein 2 / Monocyte chemotactic protein 2 / MCP-2 / Small-inducible cytokine A8 / Monocyte chemoattractant protein 3 / Monocyte chemotactic protein 3 / MCP-3 / NC28 / Small-inducible cytokine A7


Mass: 8906.425 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CCL8, MCP2, SCYA10, SCYA8, CCL7, MCP3, SCYA6, SCYA7 / Production host: Escherichia coli (E. coli) / References: UniProt: P80075, UniProt: P80098
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.86 Å3/Da / Density % sol: 57.04 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M TRIS 8.5 pH (Buffer) 2 M (NH4)2SO4 (Precipitant)

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 6, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.39→42.38 Å / Num. obs: 16549 / % possible obs: 98.1 % / Redundancy: 3.3 % / CC1/2: 0.997 / Net I/σ(I): 7.9
Reflection shellResolution: 2.39→2.48 Å / Num. unique obs: 1551 / CC1/2: 0.913

-
Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7S58

7s58


Resolution: 2.39→42.38 Å / SU ML: 0.3262 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 39.0284
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2679 826 5.02 %
Rwork0.2374 15619 -
obs0.239 16445 97.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 82.98 Å2
Refinement stepCycle: LAST / Resolution: 2.39→42.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2283 0 10 9 2302
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00972342
X-RAY DIFFRACTIONf_angle_d1.24473186
X-RAY DIFFRACTIONf_chiral_restr0.0617357
X-RAY DIFFRACTIONf_plane_restr0.0091411
X-RAY DIFFRACTIONf_dihedral_angle_d15.8621320
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_21X-RAY DIFFRACTIONTorsion NCS0.870091873847
ens_2d_24X-RAY DIFFRACTIONTorsion NCS1.36957460104
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.39-2.540.36521130.35472428X-RAY DIFFRACTION91.08
2.54-2.730.41881070.32112654X-RAY DIFFRACTION98.89
2.73-3.010.40431700.31832590X-RAY DIFFRACTION98.82
3.01-3.440.36331430.29332647X-RAY DIFFRACTION99.5
3.44-4.340.22541590.21782608X-RAY DIFFRACTION98.16
4.34-42.380.20921340.19612692X-RAY DIFFRACTION98.33
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)
11.835548625852.130078989580.8211046502912.127841272640.2880140593871.4191723494-0.05529423794030.124085575062-0.109016029220.03345189233190.281246929364-0.01212690730650.01476840675750.433561139892-0.0003847314628390.6278219387230.1086988022170.06043303514330.788309306726-0.04488669702780.4477654538357.839077252945.369318689389.79838992189
20.193671287111-0.009768263253690.1155546711670.212164191059-0.2623119548120.0154753702158-0.1361384417490.296685094812-0.4715492132820.284358481136-0.0731437915803-0.7006376072990.155614794181.01929097224-6.77763795468E-50.7094599905380.0474547924523-0.01588062810281.132116937430.01715269169380.86971796851217.08923592896.112079940086.76678614215
30.218638622649-0.0467454482077-0.1038207386440.2710123725370.006046745762260.225908812047-0.1163493996771.34555489835-0.940706574507-0.567025417895-0.0205970425432-0.4939003892170.7762511969990.6545507527440.002846616329130.734469767352-0.0734585521805-0.01073277330740.7981655260280.09401078538960.5945233453699.0966919589715.980214250811.2776802331
40.0435119407217-0.1303617363880.01472376325260.401749857872-0.02946924404210.03264223876670.08923139626240.440832567572-0.9581849162541.048509520270.232383878723-0.23798522548-0.1331107544141.902773140020.001045242072490.738122064975-0.02120058662620.1137885677560.9787068953990.05318033440070.52733194391611.508886768211.923025419420.8596365022
50.30635599595-0.2982169021960.1790447681390.4313706132450.08865907486510.212326868444-0.688774088286-0.3496913780120.05636581996290.6103080884010.580132420070.2715822174780.0787163541025-0.3566437223060.00432417523830.6153808382480.004840955317080.1027933332620.5866439113910.03890612036790.427035465372-0.6177510409613.053547222121.9611180105
60.788728833290.9793756410670.1794836814610.6666900645240.1286677388280.473186782248-0.1590666016070.6984199531921.085735369180.09378006201630.563900708054-0.35773825357-0.06166383675950.423871012101-0.0007039393216840.6874451506340.000735415080161-0.003103424680110.8204753487420.08046338352910.8719083309258.4001007122717.8792356789.03908848951
70.865069263862-1.25751022-0.05489031111241.552816011540.9407124461351.05437418223-0.2687170079590.9188128963970.00986470163612-0.3478165131360.6287879019050.422066848167-0.167474869483-0.547576602213-0.001117972720540.773955457871-0.1689562818360.005569222689040.6541962011140.05940990654270.4904556328714.1177372005617.222312498111.5132249977
80.5172884088140.417976228691-0.3346279469730.4827493492660.07501667867820.4599408591280.2117033772040.3522963428031.01651099930.59487776507-0.691058205074-1.264002700220.1140839503540.388887284343-0.003416725858270.750657339898-0.0338692845909-0.07421532957590.882098669058-0.02369959397440.95433716909427.467916908210.8864886739.622074572
90.0817778951808-0.00714301909509-0.1193329455610.195866645586-0.1573990928640.2060977990510.317797410783-0.79109885208-0.7266280779460.9841343985440.184503473303-0.7941271006461.592373614350.3301371253910.0007360096967811.02921848613-0.0399047705441-0.1775807981830.632144261099-0.1036269305181.151647246722.6656554935-8.0847274684136.8734740169
100.110860650459-0.008366891511320.006790613199070.04200278331760.05743397303230.08108296080210.6725980380550.881500339822-0.9082506546550.724753441856-0.846368935714-0.202776823511.028560641140.797802211939-0.004551151836050.7578874766980.0125792184556-0.08458085511091.16203914608-0.01414943341131.0351935109433.6858984826.5915124795739.6158678777
110.3809565212510.02734182162340.3054930860730.6061889607970.2192438812550.3579945188191.21344578494-0.0817443288454-2.185936705790.66572302564-1.005154666140.03327193161531.528249038770.7492056254580.03298699345881.047620917050.216441520217-0.3182612112720.88432248618-0.0805812965251.154801526930.8342440954-6.6974168802141.3582058584
120.193659531949-0.1313082073690.02248786725550.1178251812320.1701837050170.7792888672540.781569571679-0.101396236888-0.546473758523-0.207603241299-0.420658200566-0.106158952384-0.267918348783-0.6352260600590.0009525302371990.867029141180.237740114334-0.176767148670.921015808685-0.2138713898041.2433325351726.9845371373-7.4482247183126.1648801462
130.110783751745-0.1148080278830.01152498489510.02350926334860.1046159954380.0692270584084-0.804219672930.1894470851960.278331500660.105278171619-0.367839757275-0.245098965849-0.880683094361-0.3203219880340.0001941353069131.0673868717-0.0302682827315-0.4665866294540.875687191323-0.1288256596741.6430906830.3195264003-12.268543480537.1865459765
140.58822955619-0.539240660917-0.4877416717540.8303039229160.7917569874810.8049322623030.1067689095420.279616494811-0.7599441574670.4016925284710.2494636781170.540598125727-0.0419155259318-0.562787626176-0.0007622407937650.9031051531220.0586222528523-0.1963023373560.952787632231-0.1191064340671.4882288078928.5149736802-11.245927948536.5084850134
150.5146965313840.2066388731250.2986090439330.09134333807530.410321163033-0.21526374682-0.322081478879-0.217382187964-0.254483107044-0.06882506012940.540263979524-0.500999766777-0.1169338654880.9267604484150.002826039148260.80663116055-0.0116480547507-0.01316827327260.902944819707-0.08718095138840.92529083546120.71667841087.2579986425939.7661920429
160.431932693813-0.1255791030160.05105782332120.0169938757923-0.2518693799440.5206101889660.01633229271260.9559580045620.132847566216-0.602117743588-0.129490673032-0.967102531050.04507573707220.32104167517-0.001730007756350.701963661375-0.06756591256140.09866575365860.6716428720650.002830655457020.7517556778915.170811141515.114977776533.4302624121
17-0.0178382645483-0.08695916157110.08898003552340.308728885611-0.3968499591460.4169537345330.227908184460.733928204298-1.07192383384-0.0893900358627-0.001520226553021.27960688911-0.676434619882-0.5135759997080.001765890393170.8864630482930.04464728381310.0784061814150.9817943221510.1393318187461.1100871010614.6299742423-0.95561455142539.0574972323
181.26690969426-0.7417603849330.6957999377221.735061952070.4734798019120.733648163384-0.113962960103-0.3488679794850.434334195841-0.1191951239520.216794991002-0.6233532927520.6384182973440.677921983950.001026277447920.710258254741-0.05339615612120.007142873144060.721955872838-0.02588626284760.84643969930919.429542518112.860287328536.7861681284
190.691925788101-0.668341837483-0.147856401640.4490660395090.1267618560890.4757566108750.02265385453110.0008806960567920.2931430922510.177965453756-0.0176359394764-0.122773186707-1.225993902480.727604018663-0.0006791751318570.74155203083-0.02482517459320.05159817692340.629643475696-0.02952271334650.6734467750657.7594899566418.831367095334.3052798636
200.0599622925584-1.264894831220.5064085569530.995687534132-0.1303622788911.027629062870.1400414127590.3870034628210.1484625469980.343577625787-0.174732646725-0.2124207757950.5029964112920.1681788146110.0001076731951750.6714321137990.06973372443380.002052636733550.662999554517-0.04092247450980.6966461258734.33902317779-0.60453333672611.178410637
210.8522926944810.700171072855-0.906525598622.07687690193-0.1269061047261.317410478560.448420679753-0.182445733568-0.0909440733481-0.2601943209140.01930765477830.7809774012990.613771777352-0.338125722684-0.0001478323360330.805885152730.0715049378636-0.1108678759740.7751822691340.0005800415790350.7668879283246.56788405325-7.2150505727311.0078847982
221.639874890840.104569990306-0.530871135762-0.03347538633940.01528351071780.1409135671550.914777178963-0.759855374681-0.839578392588-0.0363517896905-0.710334820888-1.79479530362-0.4620951262840.5701778151220.01742873143021.507701752780.222250920722-0.8448270862240.37720289586-0.002695936448841.742127275124.53299005083-17.2169000298.29467583687
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain '1' and (resid 3 through 26 )1A3 - 261 - 24
22chain '1' and (resid 27 through 41 )1A27 - 4125 - 39
33chain '1' and (resid 42 through 47 )1A42 - 4740 - 45
44chain '1' and (resid 48 through 53 )1A48 - 5346 - 51
55chain '1' and (resid 54 through 59 )1A54 - 5952 - 57
66chain '1' and (resid 60 through 70 )1A60 - 7058 - 68
77chain '1' and (resid 71 through 85 )1A71 - 8569 - 83
88chain '3' and (resid 2 through 12 )3B2 - 121 - 11
99chain '3' and (resid 13 through 26 )3B13 - 2612 - 25
1010chain '3' and (resid 27 through 36 )3B27 - 3626 - 35
1111chain '3' and (resid 37 through 47 )3B37 - 4736 - 46
1212chain '3' and (resid 48 through 59 )3B48 - 5947 - 58
1313chain '3' and (resid 60 through 68 )3B60 - 6859 - 67
1414chain '3' and (resid 69 through 85 )3B69 - 8568 - 84
1515chain '4' and (resid 6 through 21 )4C6 - 211 - 16
1616chain '4' and (resid 22 through 30 )4C22 - 3017 - 25
1717chain '4' and (resid 31 through 40 )4C31 - 4026 - 35
1818chain '4' and (resid 41 through 57 )4C41 - 5736 - 52
1919chain '4' and (resid 58 through 76 )4C58 - 7653 - 71
2020chain '2' and (resid 1 through 21 )2D1 - 211 - 21
2121chain '2' and (resid 22 through 57 )2D22 - 5722 - 57
2222chain '2' and (resid 58 through 68 )2D58 - 6858 - 68

+
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