[English] 日本語
Yorodumi
- PDB-6tb2: Structure of human haptoglobin-hemoglobin bound to S. aureus IsdH -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6tb2
TitleStructure of human haptoglobin-hemoglobin bound to S. aureus IsdH
Components
  • Cell wall surface anchor family protein
  • Haptoglobin
  • Hemoglobin subunit alpha
  • Hemoglobin subunit beta
KeywordsMETAL TRANSPORT / Hemoglobin receptor / heme acquisition / inhibitor
Function / homology
Function and homology information


negative regulation of hydrogen peroxide catabolic process / negative regulation of oxidoreductase activity / cell wall / nitric oxide transport / hemoglobin binding / immune system process / hemoglobin alpha binding / haptoglobin binding / haptoglobin-hemoglobin complex / renal absorption ...negative regulation of hydrogen peroxide catabolic process / negative regulation of oxidoreductase activity / cell wall / nitric oxide transport / hemoglobin binding / immune system process / hemoglobin alpha binding / haptoglobin binding / haptoglobin-hemoglobin complex / renal absorption / organic acid binding / hemoglobin complex / antioxidant activity / oxygen transport / Scavenging of heme from plasma / endocytic vesicle lumen / blood vessel diameter maintenance / acute-phase response / hydrogen peroxide catabolic process / oxygen carrier activity / Late endosomal microautophagy / Heme signaling / carbon dioxide transport / response to hydrogen peroxide / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / Cytoprotection by HMOX1 / defense response / oxygen binding / regulation of blood pressure / platelet aggregation / Chaperone Mediated Autophagy / peroxidase activity / specific granule lumen / positive regulation of nitric oxide biosynthetic process / tertiary granule lumen / Factors involved in megakaryocyte development and platelet production / ficolin-1-rich granule lumen / blood microparticle / defense response to bacterium / iron ion binding / serine-type endopeptidase activity / heme binding / Neutrophil degranulation / extracellular space / extracellular exosome / extracellular region / membrane / metal ion binding / cytosol
Similarity search - Function
Iron-regulated surface determinant protein H / NEAT domain / Iron Transport-associated domain / NEAT domain profile. / NEAr Transporter domain / NEAT domain superfamily / YSIRK type signal peptide / Sushi/SCR/CCP domain / Sushi/CCP/SCR domain profile. / Sushi/SCR/CCP superfamily ...Iron-regulated surface determinant protein H / NEAT domain / Iron Transport-associated domain / NEAT domain profile. / NEAr Transporter domain / NEAT domain superfamily / YSIRK type signal peptide / Sushi/SCR/CCP domain / Sushi/CCP/SCR domain profile. / Sushi/SCR/CCP superfamily / Hemoglobin, pi / YSIRK Gram-positive signal peptide / Hemoglobin, alpha-type / Hemoglobin, beta-type / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Globin/Protoglobin / Globins / Globin domain profile. / Globin-like / Globin / Globin / Globin-like superfamily / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Haptoglobin receptor A / Haptoglobin / Hemoglobin subunit beta / Hemoglobin subunit alpha / Iron-regulated surface determinant protein H
Similarity search - Component
Biological speciesHomo sapiens (human)
Staphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsMikkelsen, J.H. / Andersen, C.B.F.
Funding support Denmark, 1items
OrganizationGrant numberCountry
LundbeckfondenR191-2015-733 Denmark
CitationJournal: To Be Published
Title: Haptoglobin is an inhibitor of Staphylococcus aureus IsdH-mediated heme-sequestering
Authors: Mikkelsen, J.H. / Runager, K.S. / Andersen, C.B.F.
History
DepositionOct 31, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 18, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: 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 / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr2_label_alt_id / _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_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn_type.id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Hemoglobin subunit alpha
B: Hemoglobin subunit beta
C: Haptoglobin
D: Cell wall surface anchor family protein
E: Cell wall surface anchor family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,0057
Polymers142,7725
Non-polymers1,2332
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11450 Å2
ΔGint-83 kcal/mol
Surface area55140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.100, 86.770, 217.950
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

#1: Protein Hemoglobin subunit alpha / Alpha-globin / Hemoglobin alpha chain


Mass: 15150.353 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P69905
#2: Protein Hemoglobin subunit beta / Beta-globin / Hemoglobin beta chain


Mass: 15890.198 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P68871
#3: Protein Haptoglobin / Zonulin


Mass: 29787.883 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HP / Plasmid: pcDNA5 / Cell line (production host): CHO / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P00738
#4: Protein Cell wall surface anchor family protein / Haptoglobin-binding heme uptake protein HarA / Heme transporter HarA


Mass: 40971.746 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria)
Gene: isdH, EP54_00915, EQ90_06455, HMPREF3211_02292, NCTC10654_01789
Plasmid: pET22B(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0E8IWL6, UniProt: Q2FXJ2*PLUS
#5: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.78 Å3/Da / Density % sol: 55.83 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.2 M sodium citrate tribasic dihydrate, 20 % w/v PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 19, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→78.46 Å / Num. obs: 35967 / % possible obs: 100 % / Redundancy: 12.9 % / Biso Wilson estimate: 117.56 Å2 / Rrim(I) all: 0.084 / Net I/σ(I): 15.12
Reflection shellResolution: 2.9→3 Å / Num. unique obs: 3445 / Rrim(I) all: 2.96

-
Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4WJG,4XS0

4wjg

4xs0


Resolution: 2.9→78.46 Å / SU ML: 0.4993 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 32.5822
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2701 1994 5.54 %
Rwork0.235 33969 -
obs0.237 35963 99.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 134.36 Å2
Refinement stepCycle: LAST / Resolution: 2.9→78.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9621 0 86 0 9707
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006410003
X-RAY DIFFRACTIONf_angle_d1.134513632
X-RAY DIFFRACTIONf_chiral_restr0.06271491
X-RAY DIFFRACTIONf_plane_restr0.00611739
X-RAY DIFFRACTIONf_dihedral_angle_d8.245936
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-2.970.39251280.41992128X-RAY DIFFRACTION89.03
2.97-3.050.43271430.39422362X-RAY DIFFRACTION100
3.05-3.140.39081430.35922421X-RAY DIFFRACTION100
3.14-3.240.38931350.34812432X-RAY DIFFRACTION100
3.24-3.360.34081490.31972425X-RAY DIFFRACTION100
3.36-3.490.31461350.32022401X-RAY DIFFRACTION100
3.49-3.650.33311490.30282444X-RAY DIFFRACTION99.96
3.65-3.840.34691380.28932407X-RAY DIFFRACTION100
3.84-4.080.3051470.26552428X-RAY DIFFRACTION100
4.08-4.40.30711440.23892451X-RAY DIFFRACTION100
4.4-4.840.2371400.20492474X-RAY DIFFRACTION100
4.84-5.540.27291440.21212465X-RAY DIFFRACTION100
5.54-6.980.25851480.25152494X-RAY DIFFRACTION99.85
6.98-78.460.2111510.17942637X-RAY DIFFRACTION99.71
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)
16.02043496112-4.445729500472.9839631012210.2478965403-1.763502475373.189611547510.249580618532-0.0019983763755-0.873530628373-0.119398524844-0.06605587532161.39259847950.276020603595-0.227668160909-0.1557359142080.5411354950680.02750213345730.1746273287211.051725134560.189301090750.8528221270282.83003253575-5.69143662869-26.7295558862
210.0367638461-3.7818146464.033016252163.156177066640.4983159511274.170509084120.693875066669-0.141535983497-0.655285018770.01621957271690.1957714702040.480361650291.689711626240.929876400892-0.5100888042331.188795864010.04667081368850.2943306749340.9999815132170.1953592764581.0069958727616.3661434304-17.2544971003-17.4689208041
38.569399402430.888320366963-1.126981037546.261602208640.9168279960635.06600683796-0.483476094967-1.25323662893-2.07349569873.18323523316-0.3775082450480.4653674192151.08182991958-0.6258083407310.2367623616730.982837216473-0.1003522885830.3101228555421.321531155040.2259460549641.17945462643.68632458929-12.4747117491-15.4889216875
42.14951090996-0.837689464434-0.1446863844415.792194723660.4853676752745.70487592822-0.889531015266-1.969652599191.746228253921.347647039790.413482012379-0.788217533952-1.11956365009-0.8459506742910.03231691805081.1892367253-0.01734985573450.1695331684361.109341029340.02751326444811.075339624912.53619882550.729752864087-13.2401949364
56.35273113373-0.2134341576030.5031003607215.364006208430.1966704863474.810607215380.4991222820860.7733848765080.2607684214660.210074455764-0.2539135362890.242612170332-0.00444151595251-0.2265395126080.06516784579590.6799836375410.07300266703070.2931341375940.8205220822890.1594264341690.83969693561410.4591498256-4.51492867386-26.8571999225
65.41487547601-5.1215162314-1.430262570879.2804382839-3.598354003095.537933572010.550007709760.0325975084956-1.586074496141.56291067933-0.3699486994650.955087696425-0.9856590102440.2885888923410.1986533233051.21915648701-0.244151138974-0.00852204089231.17548355648-0.003235916098291.1270644208813.7939936643-28.3053714195-37.4365398929
78.48730270473.042501350271.913649752985.612139710331.934656604744.339444411220.02980155140871.623078514820.584101887737-0.8971846284690.256644838744-0.380342553798-0.6389402786570.899055145061-0.2870108896380.8247302792470.1961492052970.2048309175991.194786110770.2960685419020.99783443271814.8971140063-2.69376219742-45.9152250581
82.818100667713.077971600170.07278100465319.10058442904-4.070022997183.90013766663-0.8733000108910.181195593339-0.490686686223-1.290806712190.877727273155-2.97409859593-0.1167472118450.229013691714-0.04451542009491.23223383950.09110605714040.1433614877041.48164372865-0.3712937089021.4200704867923.6405302374-17.0615471885-46.8841443334
93.7144541785-0.921811188062.132323451577.746013082372.077836805627.75958822137-0.113808672304-0.1117518764680.694407963224-0.7809251449860.152497546305-0.732216950960.1543108520530.0314176898719-0.03382103709510.6157910616240.13137003750.1928963158080.8068005494380.1162194392930.76116913246518.6309578204-15.0864455717-37.2926222626
104.252213014573.82295250163-0.3982743880034.96464216682-2.660769517074.76421237117-0.04673374225380.266118035901-0.6833337616660.2276202274490.133026984576-0.738168927616-0.1191141873890.428194906238-0.212365705410.8066430996580.04551865815330.194780136430.8471814483190.01573737449471.0909683526538.90678195051.63556370906-29.4181699881
114.77691618521.810170972561.597460626864.191042587831.518447580856.454526564390.260886791014-1.001466177430.2884459715261.322164637270.175163583577-0.2925861042220.58955647634-0.601714741364-0.5245567149280.9660156746730.00265612571784-0.03877608834490.937381821998-0.01661102399911.0726646210740.65240053644.06084678537-11.5053478095
125.950140742022.66453492251.579051361245.887189139060.2451803030933.67545741666-0.4251427629130.336122308873-0.7830691983370.8954538688180.372362650277-0.8169682981671.990090597611.98420966613-0.03237711025181.00375301560.203406796310.07374650716331.142221563950.03177037784721.5805865620645.1193197733-5.60191542049-21.3373938756
135.89751851792.185021736542.741095929587.26970446786-2.446103423797.625013501240.7651067027640.3532509246790.1173976678450.0756199203061-0.222164298028-0.7076078756290.2651185152280.87781095267-0.5218742024490.888485577596-0.0176240114925-0.009701058284110.850867967381-0.02605551821370.93557511449545.86607599536.75852921161-18.3071885168
144.512780376161.54691920612-3.342590281592.44080003757-1.374321751366.564346876670.1671762745870.05281604377030.6240982268020.1670337115440.03436069363290.00300919041943-0.3914604814850.134316025181-0.211333596190.7289125597870.09941293415370.1942248697920.8268724293790.05887718316370.99826868943331.8147442957.68881668241-30.5277455831
158.2772402826-0.4464879401562.037624775213.718180415342.11003807591.677301433690.422511590776-0.2155092190512.40855418370.033767099980.2771673228470.135508346477-0.555475747919-0.0946559621492-0.6115840405851.132470430830.04824364635970.4307501688711.04423092966-0.04187212490141.458812764521.113085386219.6855167137-18.3010046381
165.8128310621-0.5828034092334.812758315683.515695742232.376062257044.858191300080.01046979266480.7136246416480.719269062617-0.4079370748130.0309852049297-0.756635995013-0.166085142339-0.0237719875044-0.02967870607990.6747071131740.131798082450.3804841572430.9795077700890.2345967137141.348624496432.022805420410.2737165154-32.3882982772
178.59507028721-2.01302534804-0.9373833757784.65102864381-1.07212023411.987427469960.1145071792290.385525250140.9790657720570.45212644460.253342667565-0.553164438169-0.8106979173990.342704154426-0.350789210710.939569671478-0.03227313679390.3408669273330.819717378687-0.07447343677251.0535115442237.093152415713.94545523-21.5800107888
183.008445977620.8430674714191.758083644171.99756401525-0.3141408896056.137646309110.188949327355-0.02876688607290.4825166726590.247593288348-0.3359091268480.263486101364-0.275294012847-0.4677967104070.2005017805990.7545030088960.1199194669430.2953976407160.9183012447530.1763282455371.375535247-8.8095520776615.7493042676-19.9719230305
195.30663379515.50387500718-2.400311897656.59652725823-5.048013232526.00166762045-0.128903910568-0.266575979741-0.960893206706-0.333961629305-0.634919547084-1.127720905690.06140150405841.010302819820.7059171626690.8428374737170.03391950488270.03788299244351.000272207950.2028237876440.947796854471-2.92167067467-15.57973845178.68919101338
207.36737186121-1.33972360794-3.127751407355.207378979492.459201838085.951447779750.006880033534390.386759537544-0.665147924188-0.1092785487830.08435944434710.5877609997280.588848413754-0.00132553538082-0.07636662153750.768282179404-0.1131671456410.04770099558230.88516954599-0.08701546966621.2930001242917.2965924336-41.360919056-51.0018507949
213.260481085-0.706202200361-2.462164378457.58883949535-1.103883220241.662185197190.5546025012590.6950586856471.21345476901-1.673945760320.173336567099-1.27830047885-1.07645240841-0.15132483302-0.8015480859672.08021954692-0.008063328070530.7018343294581.57911912615-0.09699966262481.5186043825830.7230394587-3.61117845613-67.8649783847
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 35 )
2X-RAY DIFFRACTION2chain 'A' and (resid 36 through 43 )
3X-RAY DIFFRACTION3chain 'A' and (resid 44 through 71 )
4X-RAY DIFFRACTION4chain 'A' and (resid 72 through 94 )
5X-RAY DIFFRACTION5chain 'A' and (resid 95 through 141 )
6X-RAY DIFFRACTION6chain 'B' and (resid 1 through 17 )
7X-RAY DIFFRACTION7chain 'B' and (resid 18 through 57 )
8X-RAY DIFFRACTION8chain 'B' and (resid 58 through 94 )
9X-RAY DIFFRACTION9chain 'B' and (resid 95 through 146 )
10X-RAY DIFFRACTION10chain 'C' and (resid 148 through 190 )
11X-RAY DIFFRACTION11chain 'C' and (resid 191 through 220 )
12X-RAY DIFFRACTION12chain 'C' and (resid 221 through 232 )
13X-RAY DIFFRACTION13chain 'C' and (resid 233 through 267 )
14X-RAY DIFFRACTION14chain 'C' and (resid 268 through 305 )
15X-RAY DIFFRACTION15chain 'C' and (resid 306 through 341 )
16X-RAY DIFFRACTION16chain 'C' and (resid 342 through 367 )
17X-RAY DIFFRACTION17chain 'C' and (resid 368 through 406 )
18X-RAY DIFFRACTION18chain 'D' and (resid 323 through 505 )
19X-RAY DIFFRACTION19chain 'D' and (resid 506 through 655 )
20X-RAY DIFFRACTION20chain 'E' and (resid 323 through 489 )
21X-RAY DIFFRACTION21chain 'E' and (resid 490 through 655 )

+
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://pdbjlvh1.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