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- PDB-9nnu: Crystal Structure of Ebola Envelope glycoprotein GP in complex wi... -

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Basic information

Entry
Database: PDB / ID: 9nnu
TitleCrystal Structure of Ebola Envelope glycoprotein GP in complex with compound LD4-189ZbR
Components
  • Envelope glycoprotein
  • GP2
KeywordsVIRAL PROTEIN / Ebola / small molecule / drug inhibitor / glycoprotein
Function / homology
Function and homology information


symbiont-mediated killing of host cell / host cell endoplasmic reticulum / viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / symbiont-mediated-mediated suppression of host tetherin activity / host cell cytoplasm / entry receptor-mediated virion attachment to host cell / symbiont-mediated suppression of host innate immune response / membrane raft / fusion of virus membrane with host endosome membrane ...symbiont-mediated killing of host cell / host cell endoplasmic reticulum / viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / symbiont-mediated-mediated suppression of host tetherin activity / host cell cytoplasm / entry receptor-mediated virion attachment to host cell / symbiont-mediated suppression of host innate immune response / membrane raft / fusion of virus membrane with host endosome membrane / viral envelope / lipid binding / symbiont entry into host cell / host cell plasma membrane / virion membrane / extracellular region / identical protein binding
Similarity search - Function
: / Filoviruses glycoprotein, extracellular domain / Filoviruses glycoprotein / Filovirus glycoprotein / Envelope glycoprotein GP2-like, HR1-HR2
Similarity search - Domain/homology
: / Envelope glycoprotein
Similarity search - Component
Biological speciesEbola virus - Mayinga
Zaire (virus)
1976
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 Å
AuthorsAgrawal, S. / Wilson, I.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Front Immunol / Year: 2025
Title: SuFEx-enabled high-throughput medicinal chemistry for developing potent tamoxifen analogs as Ebola virus entry inhibitors.
Authors: Dada, L. / Nagai, E. / Agrawal, S. / Wirchnianski, A.S. / Wilson, I.A. / Chandran, K. / Kitamura, S.
History
DepositionMar 6, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 30, 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: Envelope glycoprotein
B: GP2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,1238
Polymers69,9532
Non-polymers2,1696
Water00
1
A: Envelope glycoprotein
B: GP2
hetero molecules

A: Envelope glycoprotein
B: GP2
hetero molecules

A: Envelope glycoprotein
B: GP2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)216,36824
Polymers209,8606
Non-polymers6,50818
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area37780 Å2
ΔGint-102 kcal/mol
Surface area47510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.222, 114.222, 306.370
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein Envelope glycoprotein / GP1 / 2 / GP


Mass: 51031.082 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ebola virus - Mayinga, Zaire, 1976 / Strain: Mayinga-76 / Gene: GP / Production host: Homo sapiens (human) / References: UniProt: Q05320
#2: Protein GP2


Mass: 18922.320 Da / Num. of mol.: 1 / Fragment: EbzaA.19907.a.HE11 proteolyzed C-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ebola virus - Mayinga, Zaire, 1976 / Gene: GP / Production host: Homo sapiens (human) / References: UniProt: Q05320
#3: Polysaccharide alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...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: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c6-d1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#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.: 4 / 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
#5: Chemical ChemComp-A1BZF / N-{3-[(1Z)-1-{4-[2-(dimethylamino)ethoxy]phenyl}-1-phenylbut-1-en-2-yl]phenyl}-N'-[(3R)-oxolan-3-yl]sulfuric diamide


Mass: 535.697 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H37N3O4S / Feature type: SUBJECT OF INVESTIGATION
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: 3.52 Å3/Da / Density % sol: 65.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 9% PEG6000, 100 mM Sodium Citrate, pH 5.2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Nov 24, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.59→30 Å / Num. obs: 24322 / % possible obs: 99.5 % / Redundancy: 9.2 % / CC1/2: 0.99 / Net I/σ(I): 22.4
Reflection shellResolution: 2.59→2.64 Å / Num. unique obs: 1197 / CC1/2: 0.455

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Processing

Software
NameVersionClassification
PHENIX(1.21.2_5419: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.59→29.27 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2438 2014 8.31 %
Rwork0.2204 --
obs0.2224 24246 99.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.59→29.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2857 0 144 0 3001
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003
X-RAY DIFFRACTIONf_angle_d0.621
X-RAY DIFFRACTIONf_dihedral_angle_d16.3421197
X-RAY DIFFRACTIONf_chiral_restr0.043484
X-RAY DIFFRACTIONf_plane_restr0.004524
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.59-2.650.40951390.34431521X-RAY DIFFRACTION97
2.65-2.720.33481390.30831574X-RAY DIFFRACTION99
2.72-2.80.35171400.28551556X-RAY DIFFRACTION99
2.8-2.890.30041500.26391560X-RAY DIFFRACTION99
2.89-30.30751300.25481573X-RAY DIFFRACTION99
3-3.120.28661520.24381589X-RAY DIFFRACTION100
3.12-3.260.23171510.23041576X-RAY DIFFRACTION100
3.26-3.430.24251410.22551576X-RAY DIFFRACTION100
3.43-3.640.22791450.22181611X-RAY DIFFRACTION100
3.64-3.920.20411440.20311604X-RAY DIFFRACTION100
3.92-4.320.19931330.18861583X-RAY DIFFRACTION98
4.32-4.940.19891490.17251607X-RAY DIFFRACTION99
4.94-6.210.25161480.22651604X-RAY DIFFRACTION99
6.22-29.270.26321530.22931698X-RAY DIFFRACTION99

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