[English] 日本語
Yorodumi
- PDB-7z9q: CRYO-EM STRUCTURE OF SARS-COV-2 SPIKE : H11-A10 nanobody complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7z9q
TitleCRYO-EM STRUCTURE OF SARS-COV-2 SPIKE : H11-A10 nanobody complex
Components
  • Nanobody H11-A10
  • Spike glycoprotein,Fibritin
KeywordsANTIVIRAL PROTEIN / Complex / Spike glycoprotein / nanobody H11-A10
Function / homology
Function and homology information


virion component / Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion ...virion component / Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell / membrane fusion / Attachment and Entry / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / host cell surface receptor binding / symbiont-mediated suppression of host innate immune response / receptor ligand activity / endocytosis involved in viral entry into host cell / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / identical protein binding / membrane / plasma membrane
Similarity search - Function
Fibritin C-terminal / Fibritin C-terminal region / Spike glycoprotein, N-terminal domain / Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, betacoronavirus / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. ...Fibritin C-terminal / Fibritin C-terminal region / Spike glycoprotein, N-terminal domain / Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, betacoronavirus / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2 / Jelly Rolls / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Spike glycoprotein / Fibritin
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
Tequatrovirus T4
Lama glama (llama)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsWeckener, M. / Naismith, J.H.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Engineering and Physical Sciences Research CouncilP2019-0006 United Kingdom
Wellcome Trust100209/Z/12/Z United Kingdom
CitationJournal: Proc Natl Acad Sci U S A / Year: 2022
Title: Correlation between the binding affinity and the conformational entropy of nanobody SARS-CoV-2 spike protein complexes.
Authors: Halina Mikolajek / Miriam Weckener / Z Faidon Brotzakis / Jiandong Huo / Evmorfia V Dalietou / Audrey Le Bas / Pietro Sormanni / Peter J Harrison / Philip N Ward / Steven Truong / Lucile ...Authors: Halina Mikolajek / Miriam Weckener / Z Faidon Brotzakis / Jiandong Huo / Evmorfia V Dalietou / Audrey Le Bas / Pietro Sormanni / Peter J Harrison / Philip N Ward / Steven Truong / Lucile Moynie / Daniel K Clare / Maud Dumoux / Joshua Dormon / Chelsea Norman / Naveed Hussain / Vinod Vogirala / Raymond J Owens / Michele Vendruscolo / James H Naismith /
Abstract: Camelid single-domain antibodies, also known as nanobodies, can be readily isolated from naïve libraries for specific targets but often bind too weakly to their targets to be immediately useful. ...Camelid single-domain antibodies, also known as nanobodies, can be readily isolated from naïve libraries for specific targets but often bind too weakly to their targets to be immediately useful. Laboratory-based genetic engineering methods to enhance their affinity, termed maturation, can deliver useful reagents for different areas of biology and potentially medicine. Using the receptor binding domain (RBD) of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein and a naïve library, we generated closely related nanobodies with micromolar to nanomolar binding affinities. By analyzing the structure-activity relationship using X-ray crystallography, cryoelectron microscopy, and biophysical methods, we observed that higher conformational entropy losses in the formation of the spike protein-nanobody complex are associated with tighter binding. To investigate this, we generated structural ensembles of the different complexes from electron microscopy maps and correlated the conformational fluctuations with binding affinity. This insight guided the engineering of a nanobody with improved affinity for the spike protein.
History
DepositionMar 21, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 13, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 5, 2022Group: 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.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 6, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_3d_fitting_list / em_admin / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature / struct_ncs_dom_lim
Item: _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id ..._em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _em_admin.last_update / _pdbx_entry_details.has_protein_modification / _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
Revision 1.3Nov 13, 2024Group: Data collection / Category: em_admin / Item: _em_admin.last_update

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Spike glycoprotein,Fibritin
B: Spike glycoprotein,Fibritin
C: Spike glycoprotein,Fibritin
D: Nanobody H11-A10
E: Nanobody H11-A10
F: Nanobody H11-A10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)478,49452
Polymers464,2546
Non-polymers14,23946
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: isothermal titration calorimetry, surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area44280 Å2
ΔGint27 kcal/mol
Surface area153390 Å2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
32A
42C
53B
63C
74D
84E
95D
105F
116E
126F

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ALAALASERSERAAA27 - 114727 - 1147
211ALAALASERSERBBB27 - 114727 - 1147
322ALAALASERSERAAA27 - 114727 - 1147
422ALAALASERSERCCC27 - 114727 - 1147
533ALAALASERSERBBB27 - 114727 - 1147
633ALAALASERSERCCC27 - 114727 - 1147
744GLNGLNHISHISDDD1 - 1341 - 134
844GLNGLNHISHISEEE1 - 1341 - 134
955GLNGLNHISHISDDD1 - 1341 - 134
1055GLNGLNHISHISFFF1 - 1341 - 134
1166GLNGLNHISHISEEE1 - 1341 - 134
1266GLNGLNHISHISFFF1 - 1341 - 134

NCS ensembles :
IDDetails
1Local NCS retraints between domains: 1 2
2Local NCS retraints between domains: 3 4
3Local NCS retraints between domains: 5 6
4Local NCS retraints between domains: 7 8
5Local NCS retraints between domains: 9 10
6Local NCS retraints between domains: 11 12

-
Components

#1: Protein Spike glycoprotein,Fibritin / S glycoprotein / E2 / Peplomer protein / Collar protein / Whisker antigen control protein


Mass: 139877.906 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2, (gene. exp.) Tequatrovirus T4
Gene: S, 2, wac / Cell line (production host): HEK 293T Lenti-X, HEK293T / Production host: Homo (humans) / References: UniProt: P0DTC2, UniProt: P10104
#2: Antibody Nanobody H11-A10


Mass: 14873.572 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli) / Strain (production host): WK6
#3: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 20
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#4: Sugar...
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 26 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Complex between Spike and nanobody H11-A10COMPLEX#1-#20MULTIPLE SOURCES
2Spike glycoprotein trimerCOMPLEX#11RECOMBINANT
3Nanobody H11-A10COMPLEX#21RECOMBINANT
Molecular weight
IDEntity assembly-IDValue (°)Experimental value
110.52 MDaNO
210.142 MDaNO
310.015 MDaNO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Severe acute respiratory syndrome coronavirus 22697049
22Escherichia virus T410665
33Lama glama (llama)9844
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-IDStrain
12Homo sapiens (human)9606HEK 293T
22Homo sapiens (human)9606HEK 293T Lenti-X
33Escherichia coli (E. coli)562WK6
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
110 mMHEPESHEPES1
2150 mMSodium chlorideNaCl1
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER/RHODIUM / Grid type: Homemade
VitrificationInstrument: SPOTITON / Cryogen name: ETHANE / Humidity: 80 %
Details: SPT Labtech prototype 300 mesh 1.2/2.0 nanowire grids with a highly reproduceable rectangular bar cross-section were used. The grids were glow-discharged on low for 260 s (Plasma Cleaner PDC- ...Details: SPT Labtech prototype 300 mesh 1.2/2.0 nanowire grids with a highly reproduceable rectangular bar cross-section were used. The grids were glow-discharged on low for 260 s (Plasma Cleaner PDC-002-CE, Harrick Plasma) to activate the nanowires. Approximately 6 nL of the complex were applied to the grids using a Chameleon EP system (SPT Labtech) at 80% relative humidity and ambient temperature.

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS / Details: EPU auto-function coma free correction
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 81000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 1500 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: ZEMLIN TABLEAU
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 3 sec. / Electron dose: 51.5 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Details: The images were collected as 50 frame movies
EM imaging opticsEnergyfilter name: GIF Quantum LS / Energyfilter slit width: 20 eV
Image scansWidth: 5760 / Height: 4092

-
Processing

SoftwareName: REFMAC / Version: 5.8.0267 / Classification: refinement
EM software
IDNameVersionCategory
2EPUimage acquisition
4GctfCTF correction
7UCSF Chimeramodel fitting
8Cootmodel fitting
10REFMACmodel refinement
11RELION3.08initial Euler assignment
12RELION3.08final Euler assignment
13RELION3.08classification
14RELION3.083D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 3264123
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 305820 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: RECIPROCAL
Atomic model building

3D fitting-ID: 1 / Accession code: 6ZHD / Initial refinement model-ID: 1 / Pdb chain residue range: 27-1147 / PDB-ID: 6ZHD

6zhd

/ Source name: PDB / Type: experimental model

IDPdb chain-ID
1A
2B
3C
RefinementResolution: 3.6→235.32 Å / Cor.coef. Fo:Fc: 0.971 / WRfactor Rwork: 0.312 / SU B: 32.474 / SU ML: 0.466 / Average fsc overall: 0.747 / Average fsc work: 0.747 / ESU R: 0.58
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rwork0.3125 209889 -
all0.3125 --
obs--100 %
Solvent computationSolvent model: BABINET MODEL
Displacement parametersBiso mean: 313.282 Å2
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0110.01327779
ELECTRON MICROSCOPYr_bond_other_d0.0310.01525386
ELECTRON MICROSCOPYr_ext_dist_refined_d0.0310.01101983
ELECTRON MICROSCOPYr_angle_refined_deg1.4691.69537928
ELECTRON MICROSCOPYr_angle_other_deg1.5441.61658440
ELECTRON MICROSCOPYr_dihedral_angle_1_deg6.35453347
ELECTRON MICROSCOPYr_dihedral_angle_2_deg29.83522.9741318
ELECTRON MICROSCOPYr_dihedral_angle_3_deg13.488154159
ELECTRON MICROSCOPYr_dihedral_angle_4_deg15.46615119
ELECTRON MICROSCOPYr_chiral_restr0.0990.23884
ELECTRON MICROSCOPYr_gen_planes_refined0.0070.0231425
ELECTRON MICROSCOPYr_gen_planes_other0.0030.026577
ELECTRON MICROSCOPYr_nbd_refined0.2060.29918
ELECTRON MICROSCOPYr_symmetry_nbd_other0.1920.248248
ELECTRON MICROSCOPYr_nbtor_refined0.1790.227770
ELECTRON MICROSCOPYr_symmetry_nbtor_other0.0820.228626
ELECTRON MICROSCOPYr_xyhbond_nbd_refined0.160.2894
ELECTRON MICROSCOPYr_symmetry_xyhbond_nbd_other0.0680.226
ELECTRON MICROSCOPYr_mcbond_it4.24533.55913460
ELECTRON MICROSCOPYr_mcbond_other4.24533.55913459
ELECTRON MICROSCOPYr_mcangle_it7.48650.32816774
ELECTRON MICROSCOPYr_mcangle_other7.48550.32916775
ELECTRON MICROSCOPYr_scbond_it4.01134.58114319
ELECTRON MICROSCOPYr_scbond_other4.01134.58114319
ELECTRON MICROSCOPYr_scangle_it7.40651.67821151
ELECTRON MICROSCOPYr_scangle_other7.40651.67821151
ELECTRON MICROSCOPYr_lrange_it17.501840.541104975
ELECTRON MICROSCOPYr_lrange_other17.501840.536104976
ELECTRON MICROSCOPYr_ncsr_local_group_10.1010.0559754
ELECTRON MICROSCOPYr_ncsr_local_group_20.1030.0560022
ELECTRON MICROSCOPYr_ncsr_local_group_30.0870.0560978
ELECTRON MICROSCOPYr_ncsr_local_group_40.0210.058440
ELECTRON MICROSCOPYr_ncsr_local_group_50.0210.058440
ELECTRON MICROSCOPYr_ncsr_local_group_60.0210.058440
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AELECTRON MICROSCOPYLocal ncs0.100820.05013
12BELECTRON MICROSCOPYLocal ncs0.100820.05013
23AELECTRON MICROSCOPYLocal ncs0.103450.05013
24CELECTRON MICROSCOPYLocal ncs0.103450.05013
35BELECTRON MICROSCOPYLocal ncs0.087410.05014
36CELECTRON MICROSCOPYLocal ncs0.087410.05014
47DELECTRON MICROSCOPYLocal ncs0.021410.05012
48EELECTRON MICROSCOPYLocal ncs0.021410.05012
59DELECTRON MICROSCOPYLocal ncs0.021410.05012
510FELECTRON MICROSCOPYLocal ncs0.021410.05012
611EELECTRON MICROSCOPYLocal ncs0.021340.05012
612FELECTRON MICROSCOPYLocal ncs0.021340.05012
LS refinement shell

Refine-ID: ELECTRON MICROSCOPY / Num. reflection Rfree: _ / Total num. of bins used: 20 / % reflection obs: 100 %

Resolution (Å)Rfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc workWRfactor Rwork
3.6-3.6940.596155920.596155920.410.596
3.694-3.7950.502151360.502151360.5060.502
3.795-3.9050.482147360.482147360.5960.482
3.905-4.0250.476141480.476141480.6410.476
4.025-4.1570.454139360.454139360.70.454
4.157-4.3030.421133660.421133660.7660.421
4.303-4.4650.386129930.386129930.8120.386
4.465-4.6470.365124740.365124740.8420.365
4.647-4.8540.351118930.351118930.8550.351
4.854-5.0910.347114180.347114180.8570.347
5.091-5.3660.341108290.341108290.8640.341
5.366-5.6910.364102660.364102660.8520.364
5.691-6.0840.3796010.3796010.8460.37
6.084-6.5710.35590210.35590210.8420.355
6.571-7.1980.34582390.34582390.8360.345
7.198-8.0460.35574180.35574180.8370.355
8.046-9.2890.35266050.35266050.8720.352
9.289-11.3720.34355760.34355760.9010.343
11.372-16.0640.27842760.27842760.9130.278
16.064-235.320.23823650.23823650.9710.238

+
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