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- PDB-2ghw: Crystal structure of SARS spike protein receptor binding domain i... -

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Basic information

Entry
Database: PDB / ID: 2ghw
TitleCrystal structure of SARS spike protein receptor binding domain in complex with a neutralizing antibody, 80R
Components
  • Spike glycoprotein
  • anti-sars scFv antibody, 80R
KeywordsVIRUS/VIRAL PROTEIN/ANTIBIOTIC / SARS / S protein / neutralizing antibody / VIRUS-VIRAL PROTEIN-ANTIBIOTIC COMPLEX
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 / host cell plasma membrane / virion membrane / identical protein binding / membrane
Similarity search - Function
Spike protein, C-terminal core receptor binding subdomain / Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / 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 ...Spike protein, C-terminal core receptor binding subdomain / Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / 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 / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Spike glycoprotein / Single-chain Fv
Similarity search - Component
Biological speciesSARS coronavirus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 5, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE THE SEQUENCE OF ANTI-SARS SCFV ANTIBODY, 80R IS NOT AVAILABLE AT UNIPROT SEQUENCE DATABASE ...SEQUENCE THE SEQUENCE OF ANTI-SARS SCFV ANTIBODY, 80R IS NOT AVAILABLE AT UNIPROT SEQUENCE DATABASE AT THE TIME OF PROCESSING.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Spike glycoprotein
B: anti-sars scFv antibody, 80R
C: Spike glycoprotein
D: anti-sars scFv antibody, 80R
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,8549
Polymers98,6764
Non-polymers1775
Water8,467470
1
A: Spike glycoprotein
B: anti-sars scFv antibody, 80R
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,4806
Polymers49,3382
Non-polymers1424
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2820 Å2
ΔGint-41 kcal/mol
Surface area18620 Å2
MethodPISA
2
C: Spike glycoprotein
D: anti-sars scFv antibody, 80R
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,3743
Polymers49,3382
Non-polymers351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2490 Å2
ΔGint-20 kcal/mol
Surface area18600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.453, 175.902, 67.561
Angle α, β, γ (deg.)90.00, 96.55, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
31A
41C
51A
61C
12B
22D

NCS domain segments:

Refine code: 2

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111LEULEUVALVALAA322 - 3499 - 36
211LEULEUVALVALCC322 - 3499 - 36
321PHEPHEVALVALAA361 - 36948 - 56
421PHEPHEVALVALCC361 - 36948 - 56
531ASNASNGLUGLUAA381 - 50268 - 189
631ASNASNGLUGLUCC381 - 50268 - 189
112GLUGLUSERSERBB1 - 2403 - 242
212GLUGLUSERSERDD1 - 2403 - 242

NCS ensembles :
ID
1
2

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Components

#1: Protein Spike glycoprotein / 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: Antibody anti-sars scFv antibody, 80R


Mass: 26454.303 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET22b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q65ZC9
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 470 / 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: 2.87 Å3/Da / Density % sol: 57.21 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 12.5% PEG4000, 0.1M sodium acetate, 0.2M ammonium sulfate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 1.11587 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 20, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11587 Å / Relative weight: 1
ReflectionResolution: 2.29→50 Å / Num. all: 51915 / Num. obs: 51915 / % possible obs: 93.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -4 / Redundancy: 3.1 % / Rmerge(I) obs: 0.145 / Net I/σ(I): 8.8
Reflection shellResolution: 2.29→2.38 Å / Rmerge(I) obs: 0.571 / Mean I/σ(I) obs: 1.9 / % possible all: 87

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
Blu-Icedata collection
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2AJF CHAIN F, 1DZB CHAIN A

2ajf

1dzb


Resolution: 2.3→45.55 Å / Cor.coef. Fo:Fc: 0.897 / Cor.coef. Fo:Fc free: 0.848 / SU B: 37.1 / SU ML: 0.237 / Cross valid method: THROUGHOUT / ESU R: 0.408 / ESU R Free: 0.285 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29537 2308 5.1 %RANDOM
Rwork0.24843 ---
obs0.25085 43380 93.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.106 Å2
Baniso -1Baniso -2Baniso -3
1--1.64 Å20 Å20.51 Å2
2---2.58 Å20 Å2
3---4.33 Å2
Refinement stepCycle: LAST / Resolution: 2.3→45.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6614 0 5 470 7089
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0226802
X-RAY DIFFRACTIONr_bond_other_d0.0010.024620
X-RAY DIFFRACTIONr_angle_refined_deg1.2171.9479266
X-RAY DIFFRACTIONr_angle_other_deg0.853.00311135
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6625836
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.32323.141312
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.71151026
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.2681547
X-RAY DIFFRACTIONr_chiral_restr0.0730.2984
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.027672
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021503
X-RAY DIFFRACTIONr_nbd_refined0.1650.21192
X-RAY DIFFRACTIONr_nbd_other0.190.24902
X-RAY DIFFRACTIONr_nbtor_refined0.180.23162
X-RAY DIFFRACTIONr_nbtor_other0.0790.23726
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1710.2345
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0530.23
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1770.224
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1910.269
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1450.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5241.55330
X-RAY DIFFRACTIONr_mcbond_other0.0691.51699
X-RAY DIFFRACTIONr_mcangle_it0.61226760
X-RAY DIFFRACTIONr_scbond_it0.87733225
X-RAY DIFFRACTIONr_scangle_it1.3084.52506
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A930tight positional0.030.05
2B1319tight positional0.030.05
1A1487medium positional0.140.5
2B1983medium positional0.130.5
1A930tight thermal0.090.5
2B1319tight thermal0.080.5
1A1487medium thermal0.752
2B1983medium thermal0.712
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.391 169 -
Rwork0.301 2990 -
obs--87.39 %
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)
12.2784-0.68140.75472.19580.31511.3683-0.0176-0.0623-0.15420.09590.0020.04260.1855-0.00730.0156-0.1336-0.03910.066-0.1788-0.0009-0.1579-3.327-24.40415.357
22.1035-0.5523-0.82722.1672-0.28711.15550.0445-0.04940.16470.0373-0.0597-0.1275-0.17380.03460.0152-0.1368-0.032-0.0491-0.1580.0149-0.146627.22356.96315.233
33.03560.5675-0.20132.6452-0.27610.51130.0736-0.12910.2510.1468-0.0906-0.2222-0.03610.12620.0171-0.16240.00070.0469-0.1586-0.0311-0.184413.6841.8623.45
42.240.85260.20432.79060.02230.70730.0977-0.2278-0.23310.1663-0.080.2730.0181-0.1195-0.0177-0.17940.0093-0.0266-0.14410.0388-0.136410.18930.66523.425
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1BB1 - 2443 - 246
2X-RAY DIFFRACTION2CC318 - 5055 - 192
3X-RAY DIFFRACTION3DD1 - 2453 - 247
4X-RAY DIFFRACTION4AA319 - 5096 - 196

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