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- PDB-9krq: Crystal structure of ZXC21 RBD -

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Basic information

Entry
Database: PDB / ID: 9krq
TitleCrystal structure of ZXC21 RBD
ComponentsSpike glycoprotein
KeywordsVIRAL PROTEIN / ZXC21 RBD
Function / homology
Function and homology information


host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated virion attachment to host cell / 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 / host cell plasma membrane / virion membrane / membrane
Similarity search - Function
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 (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
Similarity search - Domain/homology
Biological speciesBat coronavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.08 Å
AuthorsLan, J. / Wang, C.H.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Structure / Year: 2025
Title: Structural insights into the receptor-binding domain of bat coronavirus ZXC21.
Authors: Wang, C. / Nan, X. / Deng, Y. / Fan, S. / Li, X. / Lan, J.
History
DepositionNov 28, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0May 14, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Spike glycoprotein
A: Spike glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,6743
Polymers41,4522
Non-polymers2211
Water00
1
B: Spike glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,9472
Polymers20,7261
Non-polymers2211
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Spike glycoprotein


Theoretical massNumber of molelcules
Total (without water)20,7261
Polymers20,7261
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.163, 73.772, 117.835
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Spike glycoprotein


Mass: 20726.209 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bat coronavirus / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A0A8A0R1U2
#2: 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.: 1 / Source method: obtained synthetically / 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
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 46.88 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / Details: 0.2M Sodium iodide 20% w/v PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9798 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 26, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 3.08→50 Å / Num. obs: 7333 / % possible obs: 97 % / Redundancy: 12.3 % / CC1/2: 0.974 / Net I/σ(I): 7
Reflection shellResolution: 3.08→3.19 Å / Num. unique obs: 536 / CC1/2: 0.698

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.08→31.87 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.269 720 10.01 %
Rwork0.2361 --
obs0.2394 7193 95.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.08→31.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2928 0 14 0 2942
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0123034
X-RAY DIFFRACTIONf_angle_d1.5394137
X-RAY DIFFRACTIONf_dihedral_angle_d16.4921056
X-RAY DIFFRACTIONf_chiral_restr0.077453
X-RAY DIFFRACTIONf_plane_restr0.014529
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.08-3.320.31121220.29671104X-RAY DIFFRACTION83
3.32-3.650.30351440.26691291X-RAY DIFFRACTION97
3.65-4.180.31531460.24181310X-RAY DIFFRACTION98
4.18-5.260.211500.19031354X-RAY DIFFRACTION99
5.26-31.870.25551580.23821414X-RAY DIFFRACTION98
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)
10.09210.0250.01190.0343-0.03720.0639-0.12920.1266-0.00040.00990.1242-0.10950.0730.0959-0.06710.29270.00970.03680.1558-0.05270.147679.570642.6334-3.8738
20.0023-0.00740.00530.0272-0.02480.01930.0836-0.1645-0.15350.24180.06720.23670.0582-0.32710.00030.4464-0.18110.00360.4566-0.02030.372677.606639.99028.5022
30.0021-0.00170.00110.00390.00350.0067-0.0188-0.07960.05150.0912-0.04170.04560.0478-0.009200.351-0.123-0.06220.3436-0.01090.311786.599841.607114.7546
40-0.0032-0.00790.01310.01980.04490.0248-0.0042-0.027-0.0047-0.0115-0.00630.1499-0.02810.07060.1224-0.00290.0738-0.0942-0.0565-0.132980.974131.1403-2.1133
50.05590.0080.04360.4213-0.21520.1555-0.10870.0513-0.03720.3265-0.0959-0.1165-0.0966-0.0039-0.0470.1624-0.0063-0.04580.160.00710.225182.950429.5764-1.2626
60.5261-0.06770.2030.301-0.17280.1837-0.16070.1446-0.1775-0.02560.0186-0.01880.1341-0.0585-0.28660.27480.00940.13640.1463-0.04930.130486.831626.5326-12.102
70.0049-0.0003-0.01130.0746-0.03830.0424-0.1331-0.06710.0265-0.0643-0.05320.00640.0018-0.0411-0.09380.27860.11260.0460.2038-0.01480.395789.393927.9285-19.5823
80.5343-0.25170.04720.6304-0.56270.57690.1212-0.233-0.1608-0.04650.15570.07970.0496-0.1960.20070.1539-0.10070.02150.3706-0.0820.233870.446924.2843-9.4654
90.1322-0.09040.01450.0984-0.02470.09330.0465-0.07180.01170.02260.05020.0235-0.0549-0.01890.08320.29770.08730.06050.22830.0070.086882.612536.63231.2739
100.23660.1752-0.02480.1329-0.01540.00420.0956-0.1565-0.12080.02470.0783-0.07490.119-0.00090.18280.5763-0.0148-0.32140.72090.0280.651389.643349.47914.9181
110.2219-0.06320.05890.0524-0.07120.11650.06920.02040.0193-0.0888-0.06850.0371-0.1554-0.00960.24840.2317-0.0442-0.01040.0422-0.22660.066875.462828.000124.0918
120.0721-0.14210.04260.40340.11980.3541-0.1143-0.01710.13560.0777-0.16650.0364-0.09360.0244-0.55770.1469-0.0827-0.02990.212-0.12840.193679.666924.045331.8702
130.40790.03430.07440.3009-0.30590.3513-0.06220.0313-0.0583-0.0768-0.07090.00250.1321-0.0021-0.43890.27050.04670.00890.218-0.09390.0275.280331.291540.1523
140.31650.11710.03350.23650.03180.1226-0.070.21-0.0811-0.03940.15070.02-0.0475-0.07060.00460.075-0.02320.06280.1171-0.05150.167660.172528.079825.507
150.1026-0.0230.08460.08350.00240.0735-0.01170.07580.11-0.0181-0.040.0341-0.09390.0796-0.37720.0048-0.09680.11410.00530.0910.075364.150336.518123.8037
160.0295-0.02890.00650.0274-0.01120.0187-0.1075-0.05420.02880.2811-0.0299-0.01260.0214-0.1919-00.5216-0.0184-0.0920.324-0.13690.535883.247719.091742.6625
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 329 through 353 )
2X-RAY DIFFRACTION2chain 'B' and (resid 354 through 376 )
3X-RAY DIFFRACTION3chain 'B' and (resid 377 through 389 )
4X-RAY DIFFRACTION4chain 'B' and (resid 390 through 405 )
5X-RAY DIFFRACTION5chain 'B' and (resid 406 through 439 )
6X-RAY DIFFRACTION6chain 'B' and (resid 440 through 455 )
7X-RAY DIFFRACTION7chain 'B' and (resid 456 through 468 )
8X-RAY DIFFRACTION8chain 'B' and (resid 469 through 483 )
9X-RAY DIFFRACTION9chain 'B' and (resid 484 through 493 )
10X-RAY DIFFRACTION10chain 'B' and (resid 494 through 509 )
11X-RAY DIFFRACTION11chain 'A' and (resid 329 through 349 )
12X-RAY DIFFRACTION12chain 'A' and (resid 350 through 363 )
13X-RAY DIFFRACTION13chain 'A' and (resid 364 through 389 )
14X-RAY DIFFRACTION14chain 'A' and (resid 390 through 468 )
15X-RAY DIFFRACTION15chain 'A' and (resid 469 through 493 )
16X-RAY DIFFRACTION16chain 'A' and (resid 494 through 509 )

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