[English] 日本語
Yorodumi
- PDB-7lse: Crystal structure of the human neutralizing antibody Fab fragment... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7lse
TitleCrystal structure of the human neutralizing antibody Fab fragment T025 bound to TBEV EDIII (Far Eastern Subtype)
Components
  • Envelope protein E
  • T025 Fab Heavy Chain
  • T025 Fab Light Chain
KeywordsIMMUNE SYSTEM/VIRAL PROTEIN / Tick-borne encephalitis virus / antibody / EDIII / TBEV / IMMUNE SYSTEM / IMMUNE SYSTEM-VIRAL PROTEIN complex
Function / homology
Function and homology information


flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / viral capsid / double-stranded RNA binding / nucleoside-triphosphate phosphatase / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / clathrin-dependent endocytosis of virus by host cell / methyltransferase cap1 activity ...flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / viral capsid / double-stranded RNA binding / nucleoside-triphosphate phosphatase / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / clathrin-dependent endocytosis of virus by host cell / methyltransferase cap1 activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / protein dimerization activity / host cell perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / RNA helicase / symbiont-mediated suppression of host innate immune response / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont-mediated activation of host autophagy / RNA-directed RNA polymerase / serine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell nucleus / virion membrane / structural molecule activity / ATP hydrolysis activity / proteolysis / extracellular region / ATP binding / metal ion binding / membrane
Similarity search - Function
Genome polyprotein, Flavivirus / : / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / Flavivirus non-structural protein NS4B / Flavivirus non-structural protein NS4A / Flavivirus NS2B domain profile. / mRNA cap 0 and cap 1 methyltransferase (EC 2.1.1.56 and EC 2.1.1.57) domain profile. ...Genome polyprotein, Flavivirus / : / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / Flavivirus non-structural protein NS4B / Flavivirus non-structural protein NS4A / Flavivirus NS2B domain profile. / mRNA cap 0 and cap 1 methyltransferase (EC 2.1.1.56 and EC 2.1.1.57) domain profile. / Flavivirus non-structural protein NS2A / Flavivirus non-structural protein NS2A / Flavivirus NS3, petidase S7 / Peptidase S7, Flavivirus NS3 serine protease / Flavivirus NS3 protease (NS3pro) domain profile. / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / RNA-directed RNA polymerase, flavivirus / Flavivirus RNA-directed RNA polymerase, fingers and palm domains / Flavivirus capsid protein C / Flavivirus capsid protein C / Flavivirus non-structural Protein NS1 / Flavivirus non-structural protein NS1 / Envelope glycoprotein M, flavivirus / Envelope glycoprotein M superfamily, flavivirus / Flavivirus envelope glycoprotein M / Flavivirus polyprotein propeptide / Flavivirus polyprotein propeptide superfamily / Flavivirus polyprotein propeptide / Flavivirus envelope glycoprotein E, stem/anchor domain / : / Flavivirus NS3 helicase, C-terminal helical domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily / Flavivirus glycoprotein E, immunoglobulin-like domain / Flavivirus glycoprotein, immunoglobulin-like domain / Flavivirus glycoprotein central and dimerisation domain / Flavivirus glycoprotein, central and dimerisation domains / Flaviviral glycoprotein E, central domain, subdomain 1 / Flaviviral glycoprotein E, central domain, subdomain 2 / Ribosomal RNA methyltransferase, FtsJ domain / FtsJ-like methyltransferase / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flaviviral glycoprotein E, dimerisation domain / DEAD box, Flavivirus / Flavivirus DEAD domain / helicase superfamily c-terminal domain / Immunoglobulin E-set / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / Immunoglobulins / Immunoglobulin-like / Sandwich / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Tick-borne encephalitis virus Far Eastern subtype
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.35 Å
AuthorsKeeffe, J.R. / Bjorkman, P.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: J.Exp.Med. / Year: 2021
Title: Broad and potent neutralizing human antibodies to tick-borne flaviviruses protect mice from disease.
Authors: Agudelo, M. / Palus, M. / Keeffe, J.R. / Bianchini, F. / Svoboda, P. / Salat, J. / Peace, A. / Gazumyan, A. / Cipolla, M. / Kapoor, T. / Guidetti, F. / Yao, K.H. / Elsterova, J. / ...Authors: Agudelo, M. / Palus, M. / Keeffe, J.R. / Bianchini, F. / Svoboda, P. / Salat, J. / Peace, A. / Gazumyan, A. / Cipolla, M. / Kapoor, T. / Guidetti, F. / Yao, K.H. / Elsterova, J. / Teislerova, D. / Chrdle, A. / Honig, V. / Oliveira, T. / West, A.P. / Lee, Y.E. / Rice, C.M. / MacDonald, M.R. / Bjorkman, P.J. / Ruzek, D. / Robbiani, D.F. / Nussenzweig, M.C.
History
DepositionFeb 18, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 7, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 21, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 18, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 20, 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
H: T025 Fab Heavy Chain
L: T025 Fab Light Chain
E: Envelope protein E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,6424
Polymers61,5503
Non-polymers921
Water3,639202
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4530 Å2
ΔGint-27 kcal/mol
Surface area23550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.960, 69.720, 180.200
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11E-506-

HOH

-
Components

#1: Antibody T025 Fab Heavy Chain


Mass: 24834.730 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): Expi293F / Production host: Homo sapiens (human)
#2: Antibody T025 Fab Light Chain


Mass: 23424.988 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): Expi293F / Production host: Homo sapiens (human)
#3: Protein Envelope protein E


Mass: 13290.007 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tick-borne encephalitis virus Far Eastern subtype
Strain: Sofjin / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P07720
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 202 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.91 Å3/Da / Density % sol: 57.68 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 0.1M sodium citrate tribasic dihydrate pH 5.0, 10% PEG 6000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 30, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.35→90.1 Å / Num. obs: 30383 / % possible obs: 99.2 % / Redundancy: 11.9 % / CC1/2: 0.994 / Rmerge(I) obs: 0.197 / Rpim(I) all: 0.058 / Rrim(I) all: 0.205 / Net I/σ(I): 8.6 / Num. measured all: 362021 / Scaling rejects: 39
Reflection shellResolution: 2.35→2.43 Å / Redundancy: 12.3 % / Rmerge(I) obs: 0.891 / Num. unique obs: 2950 / CC1/2: 0.853 / Rpim(I) all: 0.261 / Rrim(I) all: 0.929 / % possible all: 99.6

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
MOSFLMdata reduction
Aimless0.7.4data scaling
PHASERphasing
PHENIX1.18.2-3874refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4OGX, 6J5F

4ogx

6j5f


Resolution: 2.35→90.1 Å / SU ML: 0.2406 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.3269
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2105 1586 5.23 %
Rwork0.1726 28740 -
obs0.1745 30326 98.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.9 Å2
Refinement stepCycle: LAST / Resolution: 2.35→90.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3961 0 6 202 4169
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00774064
X-RAY DIFFRACTIONf_angle_d0.94645535
X-RAY DIFFRACTIONf_chiral_restr0.0542619
X-RAY DIFFRACTIONf_plane_restr0.006713
X-RAY DIFFRACTIONf_dihedral_angle_d18.59081457
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.430.26581580.21732574X-RAY DIFFRACTION99.45
2.43-2.510.25621410.21192579X-RAY DIFFRACTION99.74
2.51-2.620.28021650.20912560X-RAY DIFFRACTION99.49
2.62-2.730.22561390.19642552X-RAY DIFFRACTION97.22
2.73-2.880.22411390.19622596X-RAY DIFFRACTION99.82
2.88-3.060.22691520.18892596X-RAY DIFFRACTION99.75
3.06-3.30.24311310.18272582X-RAY DIFFRACTION98.15
3.3-3.630.19411320.16382637X-RAY DIFFRACTION98.93
3.63-4.150.19041490.15892640X-RAY DIFFRACTION99.61
4.15-5.230.18121430.13472639X-RAY DIFFRACTION97.65
5.23-90.10.1791370.17182785X-RAY DIFFRACTION97.66
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)
11.031285854770.4333165239620.01600800860281.003282626670.1506301452712.11897234925-0.0200677167601-0.1047810641360.3301937467420.1833854892170.0169613047263-0.00712609635773-0.2669559655820.262348216879-0.09612620504190.32172485161-0.00834127334006-0.02213553498020.213300313392-0.013127103630.335924748438-23.0415794007-18.315410508740.8096244376
24.431584348010.0002364224916271.106634289682.06586763030.2841241072635.41195081545-0.0212074743969-0.2925074436240.1346474436650.2222355538560.02755521312230.1608416821920.45204166097-0.337791378899-0.02777265700440.1939379049720.002615353221180.006853786195770.169833874801-0.04417036113170.188524228422-27.3172435758-27.581070286237.1326972072
37.994227446911.18763406167-2.50005924832.7992464952-4.308229686656.76795399559-0.08161244697770.1204564787490.0461187991292-0.2196882269940.1153589927150.6078311004030.343239022474-0.706250934430.04820920784630.323239450723-0.04050189985530.05814707067120.325377640077-0.03725602021330.294444462847-33.8839751482-25.026105859339.8192150815
43.97443194612-1.21731445547-1.114919231190.424488455980.9938094543438.56670813959-0.3614749459310.03493818023650.09344014687150.3427469417430.1873675643950.213616425853-0.0124748986183-0.6395171803590.2040419732380.292540641617-0.00705342280327-0.01867820223720.21239592004-0.0579775729980.372772140235-29.9527382807-20.993449204543.658662328
50.828227158839-0.06795870772450.6988700701990.581732224032-1.320235644033.29879299037-0.135550384409-0.081027519340.1047213682040.2453545003450.0733139130702-0.143499623878-0.5790611746210.1485421520470.06907119137560.3395961707450.0319704903422-0.04216883026920.258085677991-0.03888110758050.31837031754-18.2178073348-26.191488474248.5454549844
64.16471630867-1.22316239989-0.6022385505522.804315257611.32475134645.603478648840.1785362044990.374390630560.50853192-0.0525570814843-0.305013711058-0.442653650399-0.723519787712-0.02475284153740.1467957476720.3457118598850.00348094707831-0.07728589515320.2465745278610.04678000743170.395387986685-6.14254690353-29.483465520364.4099554042
73.69301403882-2.127617960730.1922076347652.4758882985-0.255356398273.388588227640.0642563529286-0.5532575795871.589371525770.099026170557-0.221006900737-0.69623769249-1.041557296820.07267135404240.2536114658270.733557165472-0.0208999165693-0.08466236268730.386268008532-0.03223246683350.637662847862-2.62817974403-21.494879302668.5972736903
88.459321980941.00200904993.578527712482.36050148125-0.3917015845035.15706150501-0.236803436134-0.286238645751-0.2216803530470.02655795530240.161689642601-0.2038553813150.6408487632120.4120338983550.03282613922110.4815077208670.1481889201110.06770030898360.2589291926520.045281903280.33482297178-11.7285148582-47.014065337738.3564319838
92.826335001-0.8207686580360.7128576866483.446462916670.2249518000685.21792237659-0.24275202799-0.03320634698020.072839822390.1835919683040.233990425194-0.436009150890.1712712781980.441703492976-0.01070271897080.1881464650140.0332614057841-0.01407343424760.196774823825-0.01968453222340.26116609795-13.2180265079-38.179119892831.8504408597
103.56058452563-2.07539634623-1.088562066242.995806712170.00245603202665.44138741874-0.1013201618133.57506843713E-50.2818201333150.4137130976690.195789478813-0.7140143416060.5892238419460.604608148159-0.1349321855260.3651362298730.0696527052941-0.0545684961260.198583964232-0.03102261969430.420046733674-9.71843486927-41.840771579733.5262110865
113.84882314788-2.394577358634.014594215651.59757830131-2.960310137575.991750216030.211871790529-0.240186598875-0.301005502511-0.1899594747310.0901672976410.02109395374680.599118598484-0.00376582613059-0.2264955033320.2699713307620.0414114385710.005012149396970.202986614471-0.01336491596390.304163623614-13.4684761226-42.171125296341.1403450081
122.65123138868-0.22276408924-1.612381836941.79647891154-0.3361662345366.56847669850.0587766402451-0.02027851297480.08882796119430.175102593593-0.117982068459-0.170257488483-0.01055772652840.09466289696770.05791722360360.2269436064920.0398832069127-0.07708881644920.242601183525-0.006342845184870.288589359755-6.47473734452-42.801854275770.5308560125
131.4155597223-0.5391239392850.7749204847791.796706850860.1175446090683.668881350040.05745587129090.223350987408-0.132076664517-0.106791565097-0.1356037215480.1615936334690.0587644072385-0.312691095820.03539785486010.164859129031-0.0237841884314-0.006371804554190.278327240825-0.03564712990820.205260526732-33.7882984246-31.231447562212.633624869
144.69262419765-0.2761441278952.791531655665.016760382451.54469304352.99747921398-0.06492470777980.2201517407060.219545640534-0.3116320754770.04815053224950.266099294563-0.470726633744-0.059609470730.1142264669520.3002417346260.02020125385680.02651964566060.428218769459-0.005592694167850.205163615271-38.7570050938-19.18225274479.42649107378
153.84780599818-0.1050768879992.470193843152.34957050751-0.8030110217899.063661556960.300475182631-0.0512834718566-0.203503426998-0.2183847308320.0174103231623-0.02327747459960.610846088157-0.87060209694-0.4257997951770.206112392302-0.04035931877560.0003596266026480.38986186794-0.01878894595470.238912034174-38.9543089662-31.293641655211.2834879896
164.309997973110.257876049753.15380524695.09419152044-0.1367111347119.180882302380.03264539299090.6235237170420.364535103776-0.636021886161-0.334991076437-0.240516328743-0.558833372170.2443522128130.2447525407010.2802451597990.02601422891410.02237084963890.3596380201850.02781745562630.204951619941-32.6094207541-21.86958966753.21700294175
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'H' and (resid 1 through 33 )HA1 - 331 - 33
22chain 'H' and (resid 34 through 59 )HA34 - 5934 - 60
33chain 'H' and (resid 60 through 72 )HA60 - 7261 - 73
44chain 'H' and (resid 73 through 87 )HA73 - 8774 - 91
55chain 'H' and (resid 88 through 134 )HA88 - 13492 - 134
66chain 'H' and (resid 135 through 188 )HA135 - 188135 - 188
77chain 'H' and (resid 189 through 213 )HA189 - 213189 - 213
88chain 'L' and (resid 1 through 18 )LC1 - 181 - 18
99chain 'L' and (resid 19 through 61 )LC19 - 6119 - 61
1010chain 'L' and (resid 62 through 90 )LC62 - 9062 - 90
1111chain 'L' and (resid 91 through 113 )LC91 - 11391 - 113
1212chain 'L' and (resid 114 through 213 )LC114 - 213114 - 213
1313chain 'E' and (resid 303 through 341 )ED303 - 3411 - 39
1414chain 'E' and (resid 342 through 361 )ED342 - 36140 - 59
1515chain 'E' and (resid 362 through 378 )ED362 - 37860 - 76
1616chain 'E' and (resid 379 through 395 )ED379 - 39577 - 93

+
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