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- EMDB-53938: Structure of the RhGB07 Prefusion, Closed-state trimeric spike protein -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-53938
TitleStructure of the RhGB07 Prefusion, Closed-state trimeric spike protein
Map data
Sample
  • Complex: Trimeric RhGB07 Spike
    • Protein or peptide: RhGB07 Spike- T4 foldon fusion protein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsSpike protein of RhGB07 coronavirus / VIRAL PROTEIN
Biological speciesSarbecovirus sp. RhGB07
Methodsingle particle reconstruction / cryo EM / Resolution: 2.97 Å
AuthorsLau K / Dong CN / Ekundayo B
Funding support Switzerland, 1 items
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 AL / Li Y / Upadhyay A / Ekundayo BE / Peacock TP / Lau K / Doores KJ / Bailey D
History
DepositionJun 3, 2025-
Header (metadata) releaseSep 24, 2025-
Map releaseSep 24, 2025-
UpdateSep 24, 2025-
Current statusSep 24, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53938.png

Downloads & links

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Map

FileDownload / File: emd_53938.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.38 Å/pix.
x 300 pix.
= 415. Å		1.38 Å/pix.
x 300 pix.
= 415. Å		1.38 Å/pix.
x 300 pix.
= 415. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.38333 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1634
Minimum - Maximum-0.6360616 - 0.97758377
Average (Standard dev.)0.000086828775 (±0.02343743)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 415.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_53938_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_53938_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Trimeric RhGB07 Spike

EntireName: Trimeric RhGB07 Spike
Components
  • Complex: Trimeric RhGB07 Spike
    • Protein or peptide: RhGB07 Spike- T4 foldon fusion protein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Trimeric RhGB07 Spike

SupramoleculeName: Trimeric RhGB07 Spike / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Sarbecovirus sp. RhGB07

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Macromolecule #1: RhGB07 Spike- T4 foldon fusion protein

MacromoleculeName: RhGB07 Spike- T4 foldon fusion protein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Sarbecovirus sp. RhGB07
Molecular weightTheoretical: 138.592109 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: DGCGRLSQKT QPKLEQFNSS RRGLYYFDDI FRSSLRVLTS GYFLPFGSNV TRYEVKQVPQ VPIYYDNPLV PFGHGVYFAV TEKSNVVRG WIFGSTMDNT TQSAVLVNNG THIVVNVCNF NFCADPMFAV SAGQSYKSWI YTSSTNCTYF QAFPFAIETR P NGTGPFTH ...String:
DGCGRLSQKT QPKLEQFNSS RRGLYYFDDI FRSSLRVLTS GYFLPFGSNV TRYEVKQVPQ VPIYYDNPLV PFGHGVYFAV TEKSNVVRG WIFGSTMDNT TQSAVLVNNG THIVVNVCNF NFCADPMFAV SAGQSYKSWI YTSSTNCTYF QAFPFAIETR P NGTGPFTH LREHVFRNVD GFLHVYHNYE VINVQNGLPS GFSVLRPIFK LPLGLNITYI KAVMTLFSST TSNFIAAVAS LH YVGYLQP RTMLFHFDQN GTIVDAIDCS QNPLSELKCT TKSFSLEKGI YQTSNFRVTP TTEVIRFPNV TQLCPFSDVF NRT KFPSVY AWERMSIRDC VADYAVLYNS SISFSTFECY GVSPTKLNDL CFSSVYADYF VVRGDDVKQI APGKTGVIAD YNYK LPDDF VGCVLAWNSR HVDSKQGFYY RLFRHGKIKP YQRDMSRELY SPSGTPCTTE GFNCYDPLAH YAFASPGIGT GYQPF RVVV LSFQLLNAPA TVCGPKQSTD LVKNKCVNFN FNGLTGTGVL TDSVKKFQPF QQFGRDSSDF TDSVKDPKTL EILDIT PCS YGGVSVITPG TNTSDAVAVL YQDVNCTDVP TMLHIDQVSS DWRVYAANTG GNMFQTQAGC LVGATYDNTS YECDIPV GA GVCAKFQINT GASQSSILAY TMSLGEDSNV AYSNNSIAIP TNFSISVTTE VLPVSMTKTS VDCNMYICGD STECSSLL L QYGSFCQQLN RALAGVSVEQ DKNTQDVFAQ VKSIYKVPAI KDFGGFNFSH ILPDPAKPSK RSFIEDLLYN KVTLADPGF MKQYGDCLGG VNARDLICAQ KFNGLTVLPP LLTDDMIAAY TSALVSGTAL SGYTFGAGAA LQIPFAMQMA YRFNGIGVTQ NVLYENQKQ IANQFNKAIS QIQESLTTTA TALGKLQDVI NQNAIALNTL VKQLSSNFGA ISSVLNDILS RLDPPEAEVQ I DRLITGRL QSLQTYVTQQ LIRAAEIRAS ANLAATKMSE CVLGQSKRVD FCGKGYHLMS FPQAAPHGVV FLHVTYVPSQ EQ NFTTAPA ICHKGKAHFP REGVFVTNGT HWFVTQRNFY QPEVITTENT FESGNCDVVI GIVNNTVYDP LQPELESFKE ELD KYFKNH TSPEVGFDDI SGINASVVDI KKEIAHLNEI ASKLNESLID LQELGKYEQG SGYIPEAPRD GQAYVRKDGE WVLL STFLG RSLEVLFQGP GHHHHHHHHS AWSHPQFEKG GGSGGGGSGG SAWSHPQFEK

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Macromolecule #6: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 6 / Number of copies: 18 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration2 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 120 sec.
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
SoftwareName: EPU
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average exposure time: 5.04 sec. / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 96000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 3.3.2+220824) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7zss

Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.97 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3.2+220824) / Details: Non-Uniform Refinement / Number images used: 17685
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC (ver. 3.3.2+220824)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC (ver. 3.3.2+220824)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
SoftwareName: PHENIX / Details: EMplace
DetailsModel was docked using Phenix EMPlace followed by manual building in Coot and phenix real space refine
RefinementSpace: REAL
Output model

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

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