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- PDB-9rdt: Structure of the RhGB07 Prefusion, Closed-state trimeric spike protein -

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Basic information

Entry
Database: PDB / ID: 9rdt
TitleStructure of the RhGB07 Prefusion, Closed-state trimeric spike protein
ComponentsRhGB07 Spike- T4 foldon fusion protein
KeywordsVIRAL PROTEIN / Spike protein of RhGB07 coronavirus
Biological speciesSarbecovirus sp. RhGB07
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.97 Å
AuthorsLau, K. / Dong, C.N. / Ekundayo, B.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation Switzerland
CitationJournal: Biorxiv / Year: 2025
Title: Understanding the future risk of bat coronavirus spillover into humans - correlating sarbecovirus receptor usage, host range, and antigenicity
Authors: Thakur, N. / Newman, J. / Ni, D. / Seow, J. / Hay, A.L. / Li, Y. / Upadhyay, A. / Ekundayo, B.E. / Peacock, T.P. / Lau, K. / Doores, K.J. / Bailey, D.
History
DepositionJun 3, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 24, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: RhGB07 Spike- T4 foldon fusion protein
B: RhGB07 Spike- T4 foldon fusion protein
A: RhGB07 Spike- T4 foldon fusion protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)441,35163
Polymers415,7763
Non-polymers25,57560
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "B"
d_2ens_1chain "A"
d_3ens_1chain "C"

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ASPASPLEULEUBB17 - 11281 - 1112
d_12NAGNAGNAGNAGBZA1301
d_13NAGNAGNAGNAGRR1
d_14NAGNAGNAGNAGSS1
d_15NAGNAGNAGNAGBAB1302
d_16NAGNAGNAGNAGTT1
d_17NAGNAGNAGNAGTT2
d_18NAGNAGNAGNAGBBB1303
d_19NAGNAGNAGNAGUU1
d_110NAGNAGNAGNAGUU2
d_111BMABMABMABMAUU3
d_112NAGNAGNAGNAGVV1
d_113NAGNAGNAGNAGWW1
d_114NAGNAGNAGNAGWW2
d_115NAGNAGNAGNAGXX1
d_116NAGNAGNAGNAGYY1
d_117NAGNAGNAGNAGYY2
d_118NAGNAGNAGNAGZZ1
d_119NAGNAGNAGNAGZZ2
d_120NAGNAGNAGNAGaAA1
d_121NAGNAGNAGNAGaAA2
d_122NAGNAGNAGNAGbBA1
d_123NAGNAGNAGNAGBCB1304
d_124NAGNAGNAGNAGbBA2
d_125BMABMABMABMARR2
d_126NAGNAGNAGNAGVV2
d_127NAGNAGNAGNAGBDB1305
d_128NAGNAGNAGNAGXX2
d_129NAGNAGNAGNAGBEB1306
d_130BMABMABMABMAVV3
d_131NAGNAGNAGNAGcCA1
d_132NAGNAGNAGNAGcCA2
d_133NAGNAGNAGNAGdDA1
d_134NAGNAGNAGNAGdDA2
d_135NAGNAGNAGNAGeEA1
d_136BMABMABMABMAaAA3
d_137MANMANMANMANaAA5
d_138MANMANMANMANaAA4
d_139BMABMABMABMAZZ3
d_140BMABMABMABMAWW3
d_141NAGNAGNAGNAGSS2
d_142BMABMABMABMAdDA3
d_143NAGNAGNAGNAGeEA2
d_21ASPASPLEULEUAC17 - 11281 - 1112
d_22NAGNAGNAGNAGAFB1301
d_23NAGNAGNAGNAGfFA1
d_24NAGNAGNAGNAGgGA1
d_25NAGNAGNAGNAGAGB1302
d_26NAGNAGNAGNAGhHA1
d_27NAGNAGNAGNAGhHA2
d_28NAGNAGNAGNAGAHB1303
d_29NAGNAGNAGNAGiIA1
d_210NAGNAGNAGNAGiIA2
d_211BMABMABMABMAiIA3
d_212NAGNAGNAGNAGjJA1
d_213NAGNAGNAGNAGkKA1
d_214NAGNAGNAGNAGkKA2
d_215NAGNAGNAGNAGlLA1
d_216NAGNAGNAGNAGmMA1
d_217NAGNAGNAGNAGmMA2
d_218NAGNAGNAGNAGnNA1
d_219NAGNAGNAGNAGnNA2
d_220NAGNAGNAGNAGoOA1
d_221NAGNAGNAGNAGoOA2
d_222NAGNAGNAGNAGpPA1
d_223NAGNAGNAGNAGAIB1304
d_224NAGNAGNAGNAGpPA2
d_225BMABMABMABMAfFA2
d_226NAGNAGNAGNAGjJA2
d_227NAGNAGNAGNAGAJB1305
d_228NAGNAGNAGNAGlLA2
d_229NAGNAGNAGNAGAKB1306
d_230BMABMABMABMAjJA3
d_231NAGNAGNAGNAGqQA1
d_232NAGNAGNAGNAGqQA2
d_233NAGNAGNAGNAGrRA1
d_234NAGNAGNAGNAGrRA2
d_235NAGNAGNAGNAGsSA1
d_236BMABMABMABMAoOA3
d_237MANMANMANMANoOA5
d_238MANMANMANMANoOA4
d_239BMABMABMABMAnNA3
d_240BMABMABMABMAkKA3
d_241NAGNAGNAGNAGgGA2
d_242BMABMABMABMArRA3
d_243NAGNAGNAGNAGsSA2
d_31ASPASPLEULEUCA17 - 11281 - 1112
d_32NAGNAGNAGNAGCTA1301
d_33NAGNAGNAGNAGDD1
d_34NAGNAGNAGNAGEE1
d_35NAGNAGNAGNAGCUA1302
d_36NAGNAGNAGNAGFF1
d_37NAGNAGNAGNAGFF2
d_38NAGNAGNAGNAGCVA1303
d_39NAGNAGNAGNAGGG1
d_310NAGNAGNAGNAGGG2
d_311BMABMABMABMAGG3
d_312NAGNAGNAGNAGHH1
d_313NAGNAGNAGNAGII1
d_314NAGNAGNAGNAGII2
d_315NAGNAGNAGNAGJJ1
d_316NAGNAGNAGNAGKK1
d_317NAGNAGNAGNAGKK2
d_318NAGNAGNAGNAGLL1
d_319NAGNAGNAGNAGLL2
d_320NAGNAGNAGNAGMM1
d_321NAGNAGNAGNAGMM2
d_322NAGNAGNAGNAGNN1
d_323NAGNAGNAGNAGCWA1304
d_324NAGNAGNAGNAGNN2
d_325BMABMABMABMADD2
d_326NAGNAGNAGNAGHH2
d_327NAGNAGNAGNAGCXA1305
d_328NAGNAGNAGNAGJJ2
d_329NAGNAGNAGNAGCYA1306
d_330BMABMABMABMAHH3
d_331NAGNAGNAGNAGOO1
d_332NAGNAGNAGNAGOO2
d_333NAGNAGNAGNAGPP1
d_334NAGNAGNAGNAGPP2
d_335NAGNAGNAGNAGQQ1
d_336BMABMABMABMAMM3
d_337MANMANMANMANMM5
d_338MANMANMANMANMM4
d_339BMABMABMABMALL3
d_340BMABMABMABMAII3
d_341NAGNAGNAGNAGEE2
d_342BMABMABMABMAPP3
d_343NAGNAGNAGNAGQQ2

NCS oper:
IDCodeMatrixVector
1given(-0.5014463381151, -0.8651887288739, -0.00018281280979405), (0.86518873714127, -0.50144635428395, 5.3844489004743E-5), (-0.00013825646198651, -0.00013116746219986, 0.99999998184012)491.12232210343, 132.04736700704, 0.051009572840513
2given(-0.49939909726053, 0.86637198323335, -0.0003582229322863), (-0.86637202507595, -0.49939914875885, -6.6217266230004E-5), (-0.00023626501171766, 0.0002772854842952, 0.9999999336458)131.4297387813, 490.95110765548, -0.013427060521707

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Components

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Protein , 1 types, 3 molecules CBA

#1: Protein RhGB07 Spike- T4 foldon fusion protein


Mass: 138592.109 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sarbecovirus sp. RhGB07 / Production host: Cricetulus griseus (Chinese hamster)

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Sugars , 5 types, 60 molecules

#2: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 383.349 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-Manp]{}}LINUCSPDB-CARE
#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.: 21
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: Polysaccharide
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 15
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#5: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#6: 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.: 18 / 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

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Details

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

ComponentName: Trimeric RhGB07 Spike / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Sarbecovirus sp. RhGB07
Source (recombinant)Organism: Cricetulus griseus (Chinese hamster)
Buffer solutionpH: 7.5
SpecimenConc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3
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 magnification: 96000 X / Nominal defocus max: 2400 nm / Nominal defocus min: 1000 nm / C2 aperture diameter: 50 µm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 5.04 sec. / Electron dose: 60 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategoryDetails
2EPUimage acquisition
4cryoSPARC3.3.2+220824CTF correction
7PHENIXmodel fittingEMplace
9cryoSPARC3.3.2+220824initial Euler assignment
10cryoSPARC3.3.2+220824final Euler assignment
12cryoSPARC3.3.2+2208243D reconstruction
13PHENIXmodel refinementReal Space Refine
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C3 (3 fold cyclic)
3D reconstructionResolution: 2.97 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 17685 / Details: Non-Uniform Refinement / Symmetry type: POINT
Atomic model buildingSpace: REAL
Details: Model was docked using Phenix EMPlace followed by manual building in Coot and phenix real space refine
Atomic model buildingSource name: AlphaFold / Type: in silico model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 107.63 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.001627717
ELECTRON MICROSCOPYf_angle_d0.51737716
ELECTRON MICROSCOPYf_chiral_restr0.04574626
ELECTRON MICROSCOPYf_plane_restr0.00284701
ELECTRON MICROSCOPYf_dihedral_angle_d8.11646123
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2BBELECTRON MICROSCOPYNCS constraints1.30403086683E-12
ens_1d_3BBELECTRON MICROSCOPYNCS constraints8.8428923608679E-13

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