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- PDB-5vyh: Crystal Structure of MERS-CoV S1 N-terminal Domain -

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Basic information

Entry
Database: PDB / ID: 5vyh
TitleCrystal Structure of MERS-CoV S1 N-terminal Domain
ComponentsS proteinCoronavirus spike protein
KeywordsVIRAL PROTEIN / fusion glycoprotein / virus
Function / homology
Function and homology information


: / endocytosis involved in viral entry into host cell / 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 / membrane => GO:0016020 / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope ...: / endocytosis involved in viral entry into host cell / 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 / membrane => GO:0016020 / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / host cell plasma membrane / virion membrane / membrane
Similarity search - Function
: / Spike (S) protein S1 subunit, receptor-binding domain, MERS-CoV / Spike (S) protein S1 subunit, N-terminal domain, MERS-CoV-like / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / 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 (S) protein S1 subunit, receptor-binding domain, MERS-CoV / Spike (S) protein S1 subunit, N-terminal domain, MERS-CoV-like / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / 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
Similarity search - Domain/homology
FOLIC ACID / IMIDAZOLE / Spike glycoprotein / Spike glycoprotein
Similarity search - Component
Biological speciesMiddle East respiratory syndrome-related coronavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsWang, N. / Wrapp, D. / Pallesen, J. / Ward, A.B. / McLellan, J.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI127521 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2017
Title: Immunogenicity and structures of a rationally designed prefusion MERS-CoV spike antigen.
Authors: Jesper Pallesen / Nianshuang Wang / Kizzmekia S Corbett / Daniel Wrapp / Robert N Kirchdoerfer / Hannah L Turner / Christopher A Cottrell / Michelle M Becker / Lingshu Wang / Wei Shi / Wing- ...Authors: Jesper Pallesen / Nianshuang Wang / Kizzmekia S Corbett / Daniel Wrapp / Robert N Kirchdoerfer / Hannah L Turner / Christopher A Cottrell / Michelle M Becker / Lingshu Wang / Wei Shi / Wing-Pui Kong / Erica L Andres / Arminja N Kettenbach / Mark R Denison / James D Chappell / Barney S Graham / Andrew B Ward / Jason S McLellan /
Abstract: Middle East respiratory syndrome coronavirus (MERS-CoV) is a lineage C betacoronavirus that since its emergence in 2012 has caused outbreaks in human populations with case-fatality rates of ∼36%. ...Middle East respiratory syndrome coronavirus (MERS-CoV) is a lineage C betacoronavirus that since its emergence in 2012 has caused outbreaks in human populations with case-fatality rates of ∼36%. As in other coronaviruses, the spike (S) glycoprotein of MERS-CoV mediates receptor recognition and membrane fusion and is the primary target of the humoral immune response during infection. Here we use structure-based design to develop a generalizable strategy for retaining coronavirus S proteins in the antigenically optimal prefusion conformation and demonstrate that our engineered immunogen is able to elicit high neutralizing antibody titers against MERS-CoV. We also determined high-resolution structures of the trimeric MERS-CoV S ectodomain in complex with G4, a stem-directed neutralizing antibody. The structures reveal that G4 recognizes a glycosylated loop that is variable among coronaviruses and they define four conformational states of the trimer wherein each receptor-binding domain is either tightly packed at the membrane-distal apex or rotated into a receptor-accessible conformation. Our studies suggest a potential mechanism for fusion initiation through sequential receptor-binding events and provide a foundation for the structure-based design of coronavirus vaccines.
History
DepositionMay 25, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 30, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Mar 24, 2021Group: Source and taxonomy / Structure summary / Category: chem_comp / entity_src_gen
Item: _chem_comp.pdbx_synonyms / _entity_src_gen.pdbx_host_org_strain
Revision 1.6Apr 3, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: S protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,90912
Polymers38,5111
Non-polymers2,39811
Water7,404411
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.800, 84.370, 108.000
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Sugars , 2 types, 9 molecules A

#1: Protein S protein / Coronavirus spike protein


Mass: 38511.090 Da / Num. of mol.: 1 / Fragment: N-terminal Domain (UNP residues 18-353)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Middle East respiratory syndrome-related coronavirus
Plasmid: paH / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: T2B999, UniProt: K9N5Q8*PLUS
#2: 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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 8
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 , 4 types, 414 molecules

#3: Chemical ChemComp-FOL / FOLIC ACID / Folate


Mass: 441.397 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H19N7O6
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Chemical ChemComp-IMD / IMIDAZOLE / Imidazole


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 411 / 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: 2.95 Å3/Da / Density % sol: 58.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 6.6%(w/v) PEG 8000, 0.99%(v/v) MPD, 0.1M Imidazole/ Hydrochloric acid pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 1.18076 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Dec 3, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.18076 Å / Relative weight: 1
ReflectionResolution: 2→54 Å / Num. obs: 31311 / % possible obs: 99.3 % / Redundancy: 6.9 % / CC1/2: 0.985 / Rmerge(I) obs: 0.186 / Rpim(I) all: 0.075 / Rrim(I) all: 0.201 / Net I/σ(I): 6.1 / Num. measured all: 216171 / Scaling rejects: 500
Reflection shellResolution: 2→2.05 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.7 / CC1/2: 0.731 / Rpim(I) all: 0.325 / Rrim(I) all: 0.777 / % possible all: 92.5

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Processing

Software
NameVersionClassification
Aimless0.5.27data scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.22data extraction
iMOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: EM density

Resolution: 2→45.482 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.86
RfactorNum. reflection% reflectionSelection details
Rfree0.2217 1564 5 %random
Rwork0.1905 ---
obs0.1921 31250 99.26 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 75.33 Å2 / Biso mean: 27.7703 Å2 / Biso min: 5.55 Å2
Refinement stepCycle: final / Resolution: 2→45.482 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2703 0 157 411 3271
Biso mean--44 35.48 -
Num. residues----342
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042949
X-RAY DIFFRACTIONf_angle_d0.7654027
X-RAY DIFFRACTIONf_chiral_restr0.053448
X-RAY DIFFRACTIONf_plane_restr0.004511
X-RAY DIFFRACTIONf_dihedral_angle_d12.1961675
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0001-2.06460.29131390.25182456259593
2.0646-2.13840.2891430.23222647279099
2.1384-2.2240.25931420.217826692811100
2.224-2.32520.25781350.210326922827100
2.3252-2.44780.2271450.199726962841100
2.4478-2.60120.23851500.203826912841100
2.6012-2.8020.20981380.195627042842100
2.802-3.08390.25411270.193927312858100
3.0839-3.530.20261390.182327442883100
3.53-4.44680.20661410.159727732914100
4.4468-45.49360.181650.177928833048100
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)
10.13470.43190.54082.21452.33792.7701-0.0763-0.14550.0905-0.01610.2384-0.2484-0.21730.2062-0.17410.24890.00270.00210.20560.00880.191333.823946.072975.9047
20.3913-0.2238-0.35292.29382.39513.686-0.1483-0.0264-0.0625-0.14580.02150.0006-0.2629-0.08370.0570.08040.0055-0.00360.17510.01040.171831.708527.785356.6749
31.04490.65881.7253.44522.10075.4264-0.09150.01440.1174-0.1260.0976-0.15-0.64410.24350.04740.20010.00240.02180.2004-0.05560.17935.691846.596275.3442
41.9585-0.55290.21553.83050.9861.55270.0354-0.1554-0.0106-0.05310.1542-0.2976-0.0530.331-0.12960.18030.0119-0.00260.2496-0.07320.151937.790340.433276.9553
51.1349-0.12460.52561.50870.6231.8338-0.0408-0.1590.1956-0.0963-0.12650.1694-0.5088-0.10130.09770.32060.1043-0.07240.2067-0.05680.256125.04251.470177.3828
61.1205-0.2615-0.18012.19111.69492.004-0.0649-0.2223-0.0510.1807-0.06980.2084-0.0098-0.13760.10910.16320.043-0.01820.2125-0.03730.194822.748339.614778.3562
70.55120.4561-0.07282.15141.441.2509-0.0067-0.06290.0703-0.0047-0.04310.1038-0.1987-0.12420.00550.17330.0466-0.04150.1534-0.02090.168227.639936.94671.6607
82.39670.11050.58152.31022.98314.1417-0.04250.0282-0.11920.11740.00830.04550.00340.12960.04680.0790.02840.0230.13820.02790.143634.389926.665556.8416
93.63092.4464-1.00847.5799-0.38845.04310.10480.2074-0.31930.0884-0.08520.1093-0.1582-0.1365-0.07150.09790.03590.02410.272-0.02460.174539.464921.033643.474
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 18 through 52 )A18 - 52
2X-RAY DIFFRACTION2chain 'A' and (resid 53 through 85 )A53 - 85
3X-RAY DIFFRACTION3chain 'A' and (resid 86 through 120 )A86 - 120
4X-RAY DIFFRACTION4chain 'A' and (resid 121 through 155 )A121 - 155
5X-RAY DIFFRACTION5chain 'A' and (resid 156 through 213 )A156 - 213
6X-RAY DIFFRACTION6chain 'A' and (resid 214 through 259 )A214 - 259
7X-RAY DIFFRACTION7chain 'A' and (resid 260 through 312 )A260 - 312
8X-RAY DIFFRACTION8chain 'A' and (resid 313 through 341 )A313 - 341
9X-RAY DIFFRACTION9chain 'A' and (resid 342 through 359 )A342 - 359

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