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- PDB-4f2m: Crystal structure of a TGEV coronavirus Spike fragment in complex... -

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Basic information

Entry
Database: PDB / ID: 4f2m
TitleCrystal structure of a TGEV coronavirus Spike fragment in complex with the TGEV neutralizing monoclonal antibody 1AF10
Components
  • (monoclonal antibody 1AF10, ...) x 2
  • Spike protein
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / beta-barrel / immunoglobulin / virus entry / virus neutralization / cellular receptor / aminopeptidase N / glycosylation / virus membrane / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


: / endocytosis involved in viral entry into host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated virion attachment to host cell / membrane => GO:0016020 / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion membrane
Similarity search - Function
Coronavirus S1 glycoprotein, central receptor binding domain (RBD) / Spike glycoprotein, Alphacoronavirus / Spike glycoprotein S1, coronavirus / Coronavirus spike glycoprotein S1 / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2 / Coronavirus spike glycoprotein S1, C-terminal ...Coronavirus S1 glycoprotein, central receptor binding domain (RBD) / Spike glycoprotein, Alphacoronavirus / Spike glycoprotein S1, coronavirus / Coronavirus spike glycoprotein S1 / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
ACETIC ACID / Spike glycoprotein
Similarity search - Component
Biological speciesMus musculus (house mouse)
TGEV virulent Purdue (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsReguera, J. / Santiago, C. / Mudgal, G. / Ordono, D. / Enjuanes, L. / Casasnovas, J.M.
CitationJournal: Plos Pathog. / Year: 2012
Title: Structural bases of coronavirus attachment to host aminopeptidase N and its inhibition by neutralizing antibodies.
Authors: Reguera, J. / Santiago, C. / Mudgal, G. / Ordono, D. / Enjuanes, L. / Casasnovas, J.M.
History
DepositionMay 8, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 22, 2012Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _chem_comp.type / _database_PDB_caveat.text / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: monoclonal antibody 1AF10, heavy chain
B: monoclonal antibody 1AF10, light chain
C: monoclonal antibody 1AF10, heavy chain
D: monoclonal antibody 1AF10, light chain
E: Spike protein
F: Spike protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,67713
Polymers140,6386
Non-polymers2,0397
Water362
1
A: monoclonal antibody 1AF10, heavy chain
B: monoclonal antibody 1AF10, light chain
E: Spike protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,2286
Polymers70,3193
Non-polymers9093
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: monoclonal antibody 1AF10, heavy chain
D: monoclonal antibody 1AF10, light chain
F: Spike protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,4497
Polymers70,3193
Non-polymers1,1304
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.770, 106.050, 103.520
Angle α, β, γ (deg.)90.00, 95.13, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules EF

#3: Protein Spike protein /


Mass: 23191.023 Da / Num. of mol.: 2 / Fragment: residues 481-650
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) TGEV virulent Purdue (virus) / Strain: SC11 / Gene: S / Plasmid: pBJ5-GS / Cell line (production host): CHO Lec 3.2.8.1 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: Q0PKZ5

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Antibody , 2 types, 4 molecules ACBD

#1: Antibody monoclonal antibody 1AF10, heavy chain


Mass: 23643.396 Da / Num. of mol.: 2 / Fragment: Fab
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Description: Fab fragment prepared by papain digestion / Cell: hybridoma
#2: Antibody monoclonal antibody 1AF10, light chain


Mass: 23484.758 Da / Num. of mol.: 2 / Fragment: Fab
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Description: Fab fragment prepared by papain digestion / Cell: hybridoma

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Sugars , 2 types, 5 molecules

#4: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#6: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
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

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Non-polymers , 2 types, 4 molecules

#5: Chemical ChemComp-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 3.22 Å3/Da / Density % sol: 61.77 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 16% PEG4000, 0.2 M sodium acetate, 0.1 M 1,2,3-octanetriol isomer T, 0.1 M Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 27, 2007
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 3→25 Å / Num. all: 35787 / Num. obs: 33913 / % possible obs: 94.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.6 % / Biso Wilson estimate: 82 Å2 / Rmerge(I) obs: 0.074 / Rsym value: 0.074 / Net I/σ(I): 8.4
Reflection shellResolution: 3→3.16 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.354 / Mean I/σ(I) obs: 2 / Num. unique all: 4997 / Rsym value: 0.354 / % possible all: 95.3

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Processing

Software
NameVersionClassification
DNAdata collection
PHASERphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→25 Å / SU ML: 0.4 / σ(F): 1 / Phase error: 27.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2507 1704 5.05 %RANDOM
Rwork0.216 ---
obs0.2178 33913 94.7 %-
all-35787 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 25.586 Å2 / ksol: 0.264 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--8.9591 Å2-0 Å215.3985 Å2
2--14.9343 Å20 Å2
3----5.9752 Å2
Refinement stepCycle: LAST / Resolution: 3→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8862 0 134 2 8998
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0059226
X-RAY DIFFRACTIONf_angle_d1.20712549
X-RAY DIFFRACTIONf_dihedral_angle_d25.5985612
X-RAY DIFFRACTIONf_chiral_restr0.0811441
X-RAY DIFFRACTIONf_plane_restr0.0061582
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.04680.4021510.35652577X-RAY DIFFRACTION85
3.0468-3.09670.3921390.33782558X-RAY DIFFRACTION85
3.0967-3.150.36791250.32662597X-RAY DIFFRACTION85
3.15-3.20710.3461430.3092565X-RAY DIFFRACTION85
3.2071-3.26870.30731550.29392545X-RAY DIFFRACTION86
3.2687-3.33530.35151330.29072587X-RAY DIFFRACTION84
3.3353-3.40760.24861430.26632520X-RAY DIFFRACTION85
3.4076-3.48670.30491650.26232533X-RAY DIFFRACTION85
3.4867-3.57360.27951220.26992583X-RAY DIFFRACTION84
3.5736-3.66990.32231140.26542560X-RAY DIFFRACTION84
3.6699-3.77750.34131280.25782577X-RAY DIFFRACTION84
3.7775-3.8990.24971210.23752538X-RAY DIFFRACTION84
3.899-4.03780.251380.21662538X-RAY DIFFRACTION85
4.0378-4.19870.24851300.19852540X-RAY DIFFRACTION83
4.1987-4.38880.22431370.18082517X-RAY DIFFRACTION83
4.3888-4.61870.2211480.16762527X-RAY DIFFRACTION83
4.6187-4.9060.17391210.15522521X-RAY DIFFRACTION83
4.906-5.28130.21451520.16762889X-RAY DIFFRACTION95
5.2813-5.80650.20221510.17613012X-RAY DIFFRACTION100
5.8065-6.63240.28481480.21093012X-RAY DIFFRACTION100
6.6324-8.30270.22991680.19173020X-RAY DIFFRACTION100
8.3027-24.64270.17861620.1852880X-RAY DIFFRACTION95
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)
11.3748-0.3961-0.83041.16740.25281.09980.01010.01830.07390.01630.1054-0.0672-0.19290.123400.2288-0.0504-0.10710.2080.0450.1789-93.444318.5847102.7875
21.44371.0591-0.56960.9689-0.00750.4458-0.02920.47160.0388-0.1233-0.15740.21180.217-0.44610.00580.3557-0.1239-0.07380.3675-0.0870.3232-107.61261.951398.1823
30.9779-0.11110.00081.3940.36921.24140.1708-0.4690.47-0.03190.1927-0.059-0.32690.20870.00050.4689-0.09470.1070.2477-0.15810.3985-10.314813.408632.7423
41.2268-1.64720.0551.47740.45450.8882-0.2011-0.2259-0.22860.17560.16760.22470.3126-0.2440.01450.3086-0.1196-0.01410.247-0.03870.331-15.2107-7.265425.7649
50.54380.139-0.68740.79510.38130.73830.49720.25210.48090.6044-0.20910.9901-0.5163-0.6540.0270.4855-0.07830.2630.5153-0.01920.8123-125.704628.1846118.834
61.12550.0814-1.93051.0908-0.61232.43590.33240.81830.288-0.37350.04911.2398-0.2263-1.02031.10690.41080.1212-0.1660.92640.17531.0381-134.414425.7389105.4055
71.03970.50611.10050.96660.06312.04480.23880.04540.3756-0.26280.0908-0.4963-0.01750.7601-0.04030.5088-0.22190.21110.6325-0.18030.579321.22030.600215.6874
80.9747-0.6308-0.27610.2969-0.07140.80120.146-0.70090.2064-0.04290.1452-0.0092-0.03310.58220.00890.3582-0.0567-0.04040.5814-0.160.207120.4281-12.770423.9432
91.497-1.4135-0.9186-0.6252-0.04990.9096-0.10520.75920.0372-0.0914-0.2199-0.05370.23-0.3286-0.00010.5259-0.05910.17750.4330.01590.4864-71.2531-0.255374.8216
102.2910.0329-1.61610.755-0.06621.85490.28440.74060.36110.14590.0628-0.0164-0.4247-0.37570.05260.39640.06530.03340.7461-0.01730.2267-45.41372.350750.2086
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resid 1:122
2X-RAY DIFFRACTION2chain B and resid 1:108
3X-RAY DIFFRACTION3chain C and resid 1:122
4X-RAY DIFFRACTION4chain D and resid 1:108
5X-RAY DIFFRACTION5chain A and resid 123:219
6X-RAY DIFFRACTION6chain B and resid 109:213
7X-RAY DIFFRACTION7chain C and resid 123:220
8X-RAY DIFFRACTION8chain D and resid 109:211
9X-RAY DIFFRACTION9chain E
10X-RAY DIFFRACTION10chain F

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