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- PDB-9yyu: SARS-CoV-2 spike trimer in the early fusion intermediate conforma... -

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Basic information

Entry
Database: PDB / ID: 9yyu
TitleSARS-CoV-2 spike trimer in the early fusion intermediate conformation bound to the VN01H1 Fab (Fab local refinement)
Components
  • Spike glycoprotein
  • VN01H1 Fab heavy chain
  • VN01H1 Fab light chain
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / Virus / coronaviruses / E-FIC / ACE2 / Glycoprotein / Receptor / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


symbiont-mediated disruption of host tissue / Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular region / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / positive regulation of viral entry into host cell ...symbiont-mediated disruption of host tissue / Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular region / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / positive regulation of viral entry into host cell / membrane fusion / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / Attachment and Entry / entry receptor-mediated virion attachment to host cell / receptor-mediated virion attachment to host cell / host cell surface receptor binding / symbiont-mediated suppression of host innate immune response / endocytosis involved in viral entry into host cell / receptor ligand activity / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / symbiont entry into host cell / virion attachment to host cell / host cell plasma membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / virion membrane / membrane / identical protein binding / 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 / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, N-terminal domain superfamily / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Spike glycoprotein, betacoronavirus / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal ...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, N-terminal domain superfamily / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Spike glycoprotein, betacoronavirus / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S2 superfamily, coronavirus / 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, coronavirus / Coronavirus spike glycoprotein S2
Similarity search - Domain/homology
Biological speciesSevere acute respiratory syndrome coronavirus 2
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsPark, Y.J. / Seattle Structural Genomics Center for Infectious Disease (SSGCID) / Veesler, D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2026
Title: TMPRSS2-mediated coronavirus spike activation and inhibition.
Authors: McCallum, M. / Case, J.B. / Brown, J.T. / Park, Y.J. / Lee, J. / Sutherland, E. / Aggarwal, A. / Gibson, C. / Lempp, F.A. / Stewart, C. / Tortorici, M.A. / Sanapala, S. / Low, J.S. / ...Authors: McCallum, M. / Case, J.B. / Brown, J.T. / Park, Y.J. / Lee, J. / Sutherland, E. / Aggarwal, A. / Gibson, C. / Lempp, F.A. / Stewart, C. / Tortorici, M.A. / Sanapala, S. / Low, J.S. / Asarnow, D. / Bohan, D. / Dellota Jr., E. / Merz, B. / Chawla, B. / Kar, S. / Lanzavecchia, A. / Sallusto, F. / Riley, N.M. / Turville, S. / Purcell, L. / Diamond, M.S. / Veesler, D.
History
DepositionOct 29, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 13, 2026Provider: repository / Type: Initial release
Revision 1.0May 13, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 13, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0May 13, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 13, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 13, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 13, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Spike glycoprotein
H: VN01H1 Fab heavy chain
L: VN01H1 Fab light chain
B: Spike glycoprotein
I: VN01H1 Fab heavy chain
M: VN01H1 Fab light chain
C: Spike glycoprotein
J: VN01H1 Fab heavy chain
N: VN01H1 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)568,12612
Polymers567,4629
Non-polymers6643
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
d_1ens_1chain "C"
d_2ens_1chain "B"
d_3ens_1chain "A"
d_1ens_2chain "J"
d_2ens_2chain "I"
d_3ens_2chain "H"
d_1ens_3chain "L"
d_2ens_3chain "M"
d_3ens_3chain "N"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1LYSLYSGLYGLYCG795 - 971814 - 990
d_12ens_1NAGNAGNAGNAGCL1301
d_21ens_1LYSLYSGLYGLYBD795 - 971814 - 990
d_22ens_1NAGNAGNAGNAGBK1301
d_31ens_1LYSLYSGLYGLYAA795 - 971814 - 990
d_32ens_1NAGNAGNAGNAGAJ1301
d_11ens_2VALVALSERSERJH2 - 1222 - 122
d_21ens_2VALVALSERSERIE2 - 1222 - 122
d_31ens_2VALVALSERSERHB2 - 1222 - 122
d_11ens_3ASPASPILEILELC1 - 1071 - 107
d_21ens_3ASPASPILEILEMF1 - 1071 - 107
d_31ens_3ASPASPILEILENI1 - 1071 - 107

NCS ensembles :
ID
ens_1
ens_2
ens_3

NCS oper:
IDCodeMatrixVector
1given(-0.500004056507, 0.866023061746, 8.10525789048E-7), (-0.866023061746, -0.500004056507, -3.11033625097E-7), (1.35903890115E-7, -8.57452099714E-7, 1)169.399968119, 632.204006141, 0.000195937353169
2given(-0.500212406574, -0.865902735903, -1.62905037021E-5), (0.865902733931, -0.500212403939, -7.94803963366E-5), (6.06735806203E-5, -5.38630720197E-5, 0.999999996709)632.22768661, 169.501520414, -0.00387163838778
3given(-0.500000544688, 0.866025089307, 1.44818034807E-6), (-0.866025089308, -0.500000544688, -4.64078779219E-7), (3.22187096625E-7, -1.48620015766E-6, 0.999999999999)169.398344353, 632.203624913, 0.000346688556306
4given(-0.499998758724, -0.866026120434, 2.22598994807E-7), (0.866026120433, -0.499998758723, 1.67482365115E-6), (-1.33914180792E-6, 1.03018629054E-6, 0.999999999999)632.203328448, 169.397528964, 3.67077585395E-5
5given(-0.500002058254, -0.866024215443, -3.01616946377E-6), (0.866024215439, -0.500002058261, 2.67612263807E-6), (-3.82567794802E-6, -1.27400896632E-6, 0.999999999992)632.204315224, 169.398703032, 0.00134783791208
6given(-0.499999955, 0.866025429764, -1.44084855428E-6), (-0.86602542976, -0.499999955002, -2.39819093124E-6), (-2.79731854419E-6, 4.87161307374E-8, 0.999999999996)169.398673642, 632.203917307, 0.000754483114235

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Components

#1: Protein Spike glycoprotein / S glycoprotein / E2 / Peplomer protein


Mass: 141608.984 Da / Num. of mol.: 3 / Mutation: D614G variant, R682S, R683G
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
#2: Antibody VN01H1 Fab heavy chain


Mass: 24131.090 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody VN01H1 Fab light chain


Mass: 23413.924 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#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.: 3
Source method: isolated from a genetically manipulated source
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

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Experimental details

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Experiment

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

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1VN01H1 Fab-bound SARS-CoV-2 E-FICCOMPLEX#1-#30MULTIPLE SOURCES
2SARS-CoV-2 spike in the early fusion intermediate conformationCOMPLEX#11RECOMBINANT
3VN01H1 FabCOMPLEX#2-#31RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Severe acute respiratory syndrome coronavirus 22697049
33Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
22Homo sapiens (human)9606
33Homo sapiens (human)9606
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 200 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1Warpparticle selection
2PHENIX1.21rc1_5109model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C3 (3 fold cyclic)
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 389200 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 55.05 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00198931
ELECTRON MICROSCOPYf_angle_d0.39112189
ELECTRON MICROSCOPYf_chiral_restr0.03531398
ELECTRON MICROSCOPYf_plane_restr0.00271590
ELECTRON MICROSCOPYf_dihedral_angle_d10.98012922
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2GCELECTRON MICROSCOPYNCS constraints1.70183658468E-11
ens_1d_3GCELECTRON MICROSCOPYNCS constraints1.16118207031E-11
ens_2d_2HJELECTRON MICROSCOPYNCS constraints2.48635560924E-13
ens_2d_3HJELECTRON MICROSCOPYNCS constraints1.36672346211E-12
ens_3d_2CLELECTRON MICROSCOPYNCS constraints2.40533426743E-13
ens_3d_3CLELECTRON MICROSCOPYNCS constraints1.84453755672E-13

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