[English] 日本語
Yorodumi
- PDB-7z1c: Nanobody H11-B5 and H11-F2 bound to RBD -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7z1c
TitleNanobody H11-B5 and H11-F2 bound to RBD
Components
  • Nanobody B5
  • Nanobody F2
  • Spike protein S1
KeywordsANTIVIRAL PROTEIN / spike / nanobody / high affinity
Function / homology
Function and homology information


Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell ...Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated endocytosis of virus by host cell / membrane fusion / Attachment and Entry / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / symbiont-mediated suppression of host innate immune response / host cell surface receptor binding / 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
Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, betacoronavirus / 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 ...Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, betacoronavirus / 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 2 (HR2) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2 / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Spike glycoprotein
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsMikolajek, H. / Naismith, J.H.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Wellcome Trust100209/Z/12/Z) United Kingdom
Engineering and Physical Sciences Research CouncilEP/S025243/1 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
DepositionFeb 24, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 23, 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 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Spike protein S1
B: Nanobody F2
F: Nanobody B5
C: Spike protein S1
D: Nanobody F2
E: Nanobody B5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,31316
Polymers107,0216
Non-polymers1,29110
Water6,107339
1
A: Spike protein S1
B: Nanobody F2
F: Nanobody B5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,2629
Polymers53,5113
Non-polymers7526
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Spike protein S1
D: Nanobody F2
E: Nanobody B5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,0507
Polymers53,5113
Non-polymers5404
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.900, 56.940, 115.890
Angle α, β, γ (deg.)80.08, 87.52, 66.11
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22D
13F
23E

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRLYSLYSAA333 - 5284 - 199
21THRTHRLYSLYSCD333 - 5284 - 199
12GLNGLNSERSERBB1 - 1251 - 125
22GLNGLNSERSERDE1 - 1251 - 125
13VALVALVALVALFC2 - 1252 - 125
23VALVALVALVALEF2 - 1252 - 125

NCS ensembles :
ID
1
2
3

-
Components

-
Antibody , 2 types, 4 molecules BDFE

#2: Antibody Nanobody F2


Mass: 14833.442 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)
#3: Antibody Nanobody B5


Mass: 14960.648 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)

-
Protein / Sugars , 2 types, 4 molecules AC

#1: Protein Spike protein S1


Mass: 23716.580 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: S, 2 / Production host: Homo sapiens (human) / References: UniProt: P0DTC2
#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.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
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

-
Non-polymers , 2 types, 347 molecules

#5: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 339 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.16 Å3/Da / Density % sol: 61.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 6% v/v Tacsimate pH 6.0, 0.1 M MES monohydrate pH 6.0, 25% w/v Polyethylene glycol 4,000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 16, 2020
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.9→52 Å / Num. obs: 99469 / % possible obs: 96.4 % / Redundancy: 3.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.043 / Net I/σ(I): 10
Reflection shellResolution: 1.9→1.95 Å / Num. unique obs: 6919 / CC1/2: 0.504

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6ZBP

6zbp


Resolution: 1.9→52 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.965 / SU B: 7.657 / SU ML: 0.101 / Cross valid method: THROUGHOUT / ESU R: 0.116 / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1994 4916 4.9 %RANDOM
Rwork0.17491 ---
obs0.1761 94604 96.43 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 62.612 Å2
Baniso -1Baniso -2Baniso -3
1-1.88 Å2-1.12 Å20.05 Å2
2--0.24 Å22.79 Å2
3----1.86 Å2
Refinement stepCycle: 1 / Resolution: 1.9→52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7027 0 84 339 7450
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0137324
X-RAY DIFFRACTIONr_bond_other_d0.0010.0186605
X-RAY DIFFRACTIONr_angle_refined_deg1.3911.6559931
X-RAY DIFFRACTIONr_angle_other_deg1.2381.58215143
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0095895
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.23921.25400
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.88151098
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1591553
X-RAY DIFFRACTIONr_chiral_restr0.0580.2909
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.029038
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021922
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.5563.0073574
X-RAY DIFFRACTIONr_mcbond_other2.5543.0063573
X-RAY DIFFRACTIONr_mcangle_it3.6654.4954459
X-RAY DIFFRACTIONr_mcangle_other3.6654.4954460
X-RAY DIFFRACTIONr_scbond_it3.7253.4663750
X-RAY DIFFRACTIONr_scbond_other3.7253.4663751
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.3465.0175469
X-RAY DIFFRACTIONr_long_range_B_refined7.92734.4617793
X-RAY DIFFRACTIONr_long_range_B_other7.92934.477794
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A62730.04
12C62730.04
21B39920.02
22D39920.02
31F37380.07
32E37380.07
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.374 352 -
Rwork0.371 6668 -
obs--92.4 %
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)
12.32750.30420.37922.4205-0.28093.5868-0.009-0.099-0.3339-0.1360.07750.52020.3137-0.6077-0.06850.0764-0.0064-0.07180.18290.02330.3244-10.04-14.375-64.035
28.8113-0.1230.94483.7914-4.24697.4608-0.0499-0.14960.42190.04380.028-0.2323-0.15970.16490.02180.05880.0153-0.0360.1728-0.13360.29336.767-12.268-60.052
31.598-0.27210.37992.75930.45494.0316-0.0247-0.4551-0.2050.55210.1837-0.00380.32060.1363-0.1590.13750.0557-0.05170.20160.03810.1764.366-14.84-48.45
44.62063.5582.2756.30133.02115.0882-0.08180.084-0.3595-0.20890.14150.21920.2245-0.2935-0.05970.06780.0097-0.03890.14150.04110.2225-7.019-14.119-63.625
54.79121.8109-1.36425.4256-0.87111.7174-0.42310.0755-0.6988-0.38-0.0042-0.50810.38890.40510.42720.1940.10090.04040.30670.03670.273913.653-5.316-84.675
67.16225.5341-3.8278.6799-1.54852.59780.5352-0.26250.73130.3624-0.23280.4239-0.35790.0931-0.30250.22760.0346-0.07170.2813-0.01540.2896.5769.015-80.176
72.592.6141-1.70315.9891-2.98356.0531-0.32630.7566-0.0228-0.58660.43570.45890.1607-0.4337-0.10940.1322-0.0496-0.11890.3288-0.04680.18760.161-4.195-86.463
84.1682.9934-2.08043.0327-1.63273.1884-0.34790.4549-0.1413-0.44680.1617-0.02970.137-0.03910.18620.14610.0194-0.08820.178-0.0140.12357.571-1.542-83.501
93.8580.26020.75815.7881.84314.0256-0.13920.17190.5302-0.28140.1669-0.5702-0.62350.6241-0.02770.1438-0.05380.01430.18590.02860.30141.43319.477-77.302
102.37730.1675-0.17132.12550.32863.31240.0332-0.26380.31890.15120.025-0.4225-0.20550.4408-0.05820.07350.0079-0.07530.1372-0.0320.266137.63616.518-66.836
112.7368-0.58690.77052.64710.03653.58960.17540.466-0.1731-0.5740.0049-0.14830.32060.2124-0.18030.18540.0333-0.03760.164-0.02820.158733.7813.828-84.688
128.32951.65323.9462.34740.70034.64360.0413-0.02660.07830.00410.0114-0.3288-0.13750.3041-0.05270.05430.0186-0.00750.0761-0.01020.1736.28114.926-72.449
137.2841-1.9366-3.67956.87322.55356.37620.0073-0.3373-0.40210.1656-0.1231-0.5020.46670.03790.11580.19880.009-0.05190.17690.07730.21218.852-1.261-48.289
149.6458-0.1519-2.74223.1692-0.53533.2830.0063-0.0613-0.01310.1063-0.11320.11120.0258-0.03560.10690.165-0.0021-0.06240.1088-0.02650.101722.128.015-53.498
159.7228-2.2118-3.78021.00271.23182.73730.3334-0.28830.54870.0615-0.1796-0.1119-0.34560.1106-0.15380.3003-0.0635-0.03110.2697-0.07240.224723.6715.661-46.365
164.69082.2078-2.28161.9751-1.39013.01510.0913-0.6238-0.0720.3061-0.233-0.0622-0.01120.14740.14170.13850.0231-0.07470.1567-0.03970.102720.3756.835-50.737
174.99110.52192.02114.4743-0.06866.7651-0.10420.41930.0777-0.83590.1897-0.0342-0.050.332-0.08561.0031-0.2956-0.04850.72390.10790.120127.71914.249-118.788
181.8943-1.5289-1.504310.0546-3.023.7773-0.0887-0.09640.21470.079-0.4128-0.5145-0.31050.43170.50151.0156-0.1672-0.35790.68080.01430.464829.99613.579-103.836
192.33410.51911.35523.5299-0.42477.567-0.24050.59830.0001-0.98550.38140.22340.1680.2212-0.14090.7093-0.1575-0.10750.49980.00960.154525.1316.379-111.504
203.2998-0.97922.72480.7213-1.737415.7202-0.07290.3868-0.0089-0.3510.18530.299-0.1941-0.4005-0.11250.937-0.2232-0.22220.53240.14620.253521.00715.094-115.464
213.97580.9586-0.52813.552-0.93841.06620.41710.16830.37240.993-0.19920.8189-0.3346-0.797-0.21790.9563-0.02610.24850.92790.03120.3986-2.083-7.093-19.377
222.10020.16960.93763.21520.15258.36310.1916-0.28580.12580.8199-0.16790.2358-0.3698-0.1801-0.02370.5485-0.03030.02730.44230.05380.15026.269-6.619-22.999
2311.5571-1.4008-5.06824.1189-4.206617.64590.16010.08610.07830.23980.04640.3859-1.6457-0.4599-0.20650.49820.11040.07780.37690.04280.2421-0.9121.201-30.325
248.6674-2.625612.82662.9417-2.424720.1343-0.07130.14550.18510.3857-0.1864-0.0549-0.0885-0.01320.25770.5075-0.01160.09390.4-0.02310.14111.9550.391-11.553
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A333 - 406
2X-RAY DIFFRACTION2A407 - 418
3X-RAY DIFFRACTION3A419 - 498
4X-RAY DIFFRACTION4A499 - 528
5X-RAY DIFFRACTION5B1 - 36
6X-RAY DIFFRACTION6B37 - 46
7X-RAY DIFFRACTION7B47 - 69
8X-RAY DIFFRACTION8B70 - 125
9X-RAY DIFFRACTION9C333 - 357
10X-RAY DIFFRACTION10C358 - 407
11X-RAY DIFFRACTION11C408 - 495
12X-RAY DIFFRACTION12C496 - 528
13X-RAY DIFFRACTION13D1 - 28
14X-RAY DIFFRACTION14D29 - 56
15X-RAY DIFFRACTION15D57 - 67
16X-RAY DIFFRACTION16D68 - 125
17X-RAY DIFFRACTION17E1 - 25
18X-RAY DIFFRACTION18E26 - 37
19X-RAY DIFFRACTION19E38 - 113
20X-RAY DIFFRACTION20E114 - 126
21X-RAY DIFFRACTION21F2 - 32
22X-RAY DIFFRACTION22F33 - 112
23X-RAY DIFFRACTION23F113 - 117
24X-RAY DIFFRACTION24F118 - 126

+
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://pdbjlc1.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