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- PDB-9l9t: Crystal structure of a coronaviral M protein in complex with a C-... -

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Basic information

Entry
Database: PDB / ID: 9l9t
TitleCrystal structure of a coronaviral M protein in complex with a C-terminal peptide of the N protein
Components
  • Membrane protein
  • N protein peptide poly-Ala model
KeywordsMEMBRANE PROTEIN / M protein / N protein / interaction / coronavirus
Function / homology
Function and homology information


host cell Golgi membrane / structural constituent of virion / viral envelope / virion membrane / membrane
Similarity search - Function
M matrix/glycoprotein, MERS-like-CoV / M matrix/glycoprotein, coronavirus / Coronavirus M matrix/glycoprotein / Coronavirus membrane (Cov-M) protein profile.
Similarity search - Domain/homology
Biological speciesPipistrellus bat coronavirus HKU5
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.142 Å
AuthorsWang, X. / Sun, Z. / Zhou, X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31770783 China
CitationJournal: J.Struct.Biol. / Year: 2025
Title: Binding of an N protein peptide to M protein of a bat coronavirus.
Authors: Wang, X. / Yang, S. / Yang, P. / Sun, Z. / Zhou, X.
History
DepositionDec 31, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 5, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Membrane protein
B: Membrane protein
C: N protein peptide poly-Ala model
D: N protein peptide poly-Ala model
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,9086
Polymers50,2074
Non-polymers7012
Water28816
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.544, 220.132, 71.097
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Membrane protein / M protein / E1 glycoprotein / Matrix glycoprotein / Membrane glycoprotein


Mass: 24729.969 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pipistrellus bat coronavirus HKU5 / Gene: M, 5 / Production host: Komagataella pastoris (fungus) / References: UniProt: A3EXD6
#2: Protein/peptide N protein peptide poly-Ala model


Mass: 373.404 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Pipistrellus bat coronavirus HKU5
#3: Chemical ChemComp-N8E / 3,6,9,12,15-PENTAOXATRICOSAN-1-OL / N-OCTYLPENTAOXYETHYLENE / PENTAETHYLENE GLYCOL MONOOCTYL ETHER / OCTYLPENTAGLYCOL N-OCTYLPENTAOXYETHYLENE


Mass: 350.491 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H38O6 / Comment: C8E5, detergent*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 3.02 Å3/Da / Density % sol: 59.29 %
Crystal growTemperature: 293.15 K / Method: lipidic cubic phase / pH: 8.8
Details: 300 mM ammonium formate, 50 mM Tris-HCl pH 8.8, 35% PEG 500 MME, 7.1 mM pentaethylene glycol monooctyl ether, soaked with 1 mM VPSFEDVVDA peptide

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 25, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 3.025→20.151 Å / Num. obs: 10543 / % possible obs: 86 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.165 / Rpim(I) all: 0.081 / Rrim(I) all: 0.185 / Net I/σ(I): 7.2 / Num. measured all: 50696
Reflection shellResolution: 3.025→3.127 Å / % possible obs: 45.8 % / Redundancy: 5.8 % / Rmerge(I) obs: 1.283 / Num. measured all: 3065 / Num. unique obs: 527 / Rpim(I) all: 0.57 / Rrim(I) all: 1.407 / Net I/σ(I) obs: 1.3

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
Aimless0.7.4data scaling
XDSBUILT 20230630data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.142→20.106 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 34.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2909 486 4.7 %
Rwork0.2545 --
obs0.2563 10332 94.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.142→20.106 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3095 0 48 16 3159
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033223
X-RAY DIFFRACTIONf_angle_d0.4744375
X-RAY DIFFRACTIONf_dihedral_angle_d13.8441875
X-RAY DIFFRACTIONf_chiral_restr0.042503
X-RAY DIFFRACTIONf_plane_restr0.004523
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.142-3.59420.34971690.3153266X-RAY DIFFRACTION96
3.5942-4.51990.29541410.24683301X-RAY DIFFRACTION95
4.5199-20.1060.26591760.23483279X-RAY DIFFRACTION92
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)
10.1726-0.05180.21740.0969-0.03050.19680.1268-0.1655-0.2192-0.1894-0.0986-0.07150.05710.083500.3383-0.0156-0.02530.38860.01920.3591-16.9664-57.7798-4.8793
2-0.01160.0126-0.0066-0.0071-0.0111-0.01230.2498-0.0084-0.04410.4459-0.22970.0256-0.43550.02670.00890.40980.0530.0860.3130.13630.2888-28.0142-45.2429-13.8427
30.1983-0.1543-0.15820.11120.10580.403-0.0789-0.0365-0.0075-0.6241-0.2178-0.3511-0.5702-0.5654-0.00960.81580.0105-0.12570.51590.05890.6346-20.0582-17.0521-11.366
40.81240.2921-1.0651.5187-0.91121.59580.0508-0.33640.49610.38480.2097-0.1716-0.59770.10830.9781-0.2050.2254-0.09670.53230.14550.3818-26.6533-59.6209-2.7247
50.8518-0.89090.48760.8896-0.51060.2622-0.3979-0.24830.02310.65270.2264-0.1864-0.2554-0.0066-0.08380.30310.01250.00950.29760.0170.3901-16.295-55.86187.168
60.3805-0.8461-0.24871.71170.53680.10270.1917-0.28120.0053-0.7999-0.0981-0.0669-0.2763-0.30010.00380.350.0504-0.10150.5331-0.05340.2797-10.8491-45.07811.0647
70.61950.1507-0.64420.0562-0.19480.7686-0.07460.40980.29250.70550.1535-0.1569-0.6366-0.2670.08050.76190.067-0.1620.4013-0.07670.6877-18.9247-16.96988.4506
80.0032-0.0090.0310.0429-0.13570.42530.0746-0.00780.08760.11860.0429-0.05390.0328-0.01160.00010.86030.01740.36650.8370.04610.6004-12.2933-27.97-17.7821
90.0065-0.0112-0.05390.01730.09060.45280.0050.03890.03120.0138-0.02310.0677-0.0072-0.0220.04560.49140.0624-0.24350.7736-0.41490.7235-26.5102-27.878816.5404
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 11 through 74 )
2X-RAY DIFFRACTION2chain 'A' and (resid 75 through 117 )
3X-RAY DIFFRACTION3chain 'A' and (resid 118 through 203 )
4X-RAY DIFFRACTION4chain 'B' and (resid 11 through 43 )
5X-RAY DIFFRACTION5chain 'B' and (resid 44 through 74 )
6X-RAY DIFFRACTION6chain 'B' and (resid 75 through 117 )
7X-RAY DIFFRACTION7chain 'B' and (resid 118 through 203 )
8X-RAY DIFFRACTION8chain 'C' and (resid 1 through 5 )
9X-RAY DIFFRACTION9chain 'D' and (resid 1 through 4 )

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