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- PDB-2ghv: Crystal structure of SARS spike protein receptor binding domain -

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Basic information

Entry
Database: PDB / ID: 2ghv
TitleCrystal structure of SARS spike protein receptor binding domain
ComponentsSpike glycoproteinSpike protein
KeywordsVIRAL PROTEIN / SARS / S protein
Function / homology
Function and homology information


Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / Attachment and Entry / endocytosis involved in viral entry into host cell / SARS-CoV-1 activates/modulates innate immune responses / suppression by virus of host tetherin activity / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / membrane fusion / positive regulation of viral entry into host cell ...Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / Attachment and Entry / endocytosis involved in viral entry into host cell / SARS-CoV-1 activates/modulates innate immune responses / suppression by virus of host tetherin activity / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / membrane fusion / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / host cell plasma membrane / virion membrane / membrane / identical protein binding
Similarity search - Function
Spike protein, C-terminal core receptor binding subdomain / Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, betacoronavirus / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding ...Spike protein, C-terminal core receptor binding subdomain / Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, betacoronavirus / 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 2 (HR2) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2 / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesSARS coronavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsHwang, W.C. / Lin, Y. / Santelli, E. / Sui, J. / Jaroszewski, L. / Stec, B. / Farzan, M. / Marasco, W.A. / Liddington, R.C.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Structural basis of neutralization by a human anti-severe acute respiratory syndrome spike protein antibody, 80R.
Authors: Hwang, W.C. / Lin, Y. / Santelli, E. / Sui, J. / Jaroszewski, L. / Stec, B. / Farzan, M. / Marasco, W.A. / Liddington, R.C.
History
DepositionMar 27, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
E: Spike glycoprotein
C: Spike glycoprotein


Theoretical massNumber of molelcules
Total (without water)45,7682
Polymers45,7682
Non-polymers00
Water2,738152
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2040 Å2
ΔGint-22 kcal/mol
Surface area18560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.884, 75.884, 235.863
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
DetailsThe asymmetric unit contains a putative biological dimer

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Components

#1: Protein Spike glycoprotein / Spike protein / Peplomer protein / E2 / RBD


Mass: 22883.830 Da / Num. of mol.: 2 / Fragment: RBD of spike protein S1 (318-510)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SARS coronavirus / Genus: Coronavirus / Gene: S / Plasmid: pAcGP67A / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P59594
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 152 / Source method: isolated from a natural source / Formula: H2O

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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: 3.71 Å3/Da / Density % sol: 66.82 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 4% PEG4000, 0.1M sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.099999 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 9, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.099999 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 36084 / Num. obs: 36036 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -4 / Rsym value: 0.098
Reflection shellResolution: 2.2→2.28 Å / Mean I/σ(I) obs: 2 / Rsym value: 0.739 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
Blu-Icedata collection
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→50 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.949 / SU B: 8.696 / SU ML: 0.112 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.154 / ESU R Free: 0.144 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21312 1790 5 %RANDOM
Rwork0.18237 ---
obs0.18389 35893 99.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 49.959 Å2
Baniso -1Baniso -2Baniso -3
1-1.37 Å20 Å20 Å2
2--1.37 Å20 Å2
3----2.75 Å2
Refinement stepCycle: LAST / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2944 0 0 152 3096
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0223044
X-RAY DIFFRACTIONr_bond_other_d0.0010.022576
X-RAY DIFFRACTIONr_angle_refined_deg1.4891.9424156
X-RAY DIFFRACTIONr_angle_other_deg0.84935998
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3645364
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.20823.378148
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.00815442
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.841516
X-RAY DIFFRACTIONr_chiral_restr0.0910.2432
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023434
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02696
X-RAY DIFFRACTIONr_nbd_refined0.2050.2497
X-RAY DIFFRACTIONr_nbd_other0.1860.22571
X-RAY DIFFRACTIONr_nbtor_refined0.190.21506
X-RAY DIFFRACTIONr_nbtor_other0.0880.21749
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.2112
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1710.234
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2470.242
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3150.25
X-RAY DIFFRACTIONr_mcbond_it2.32722290
X-RAY DIFFRACTIONr_mcbond_other0.7032736
X-RAY DIFFRACTIONr_mcangle_it2.9652.52974
X-RAY DIFFRACTIONr_scbond_it3.65231531
X-RAY DIFFRACTIONr_scangle_it4.60841182
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 118 -
Rwork0.23 2477 -
obs--99.92 %
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)
13.36510.0725-0.72312.05-1.00414.87560.0498-0.43550.0380.0694-0.1121-0.0097-0.0502-0.04740.0623-0.36390.0383-0.0312-0.0302-0.0169-0.22546.8657-21.510830.8302
23.18960.99182.39993.37113.1387.2822-0.08030.19460.1717-0.807-0.01920.0899-0.53060.25250.0995-0.04050.1408-0.0429-0.12830.0645-0.20984.7603-22.4617-1.844
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1EA320 - 5027 - 189
2X-RAY DIFFRACTION2CB320 - 5027 - 189

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