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- PDB-5gmq: Structure of MERS-CoV RBD in complex with a fully human antibody MCA1 -

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Basic information

Entry
Database: PDB / ID: 5gmq
TitleStructure of MERS-CoV RBD in complex with a fully human antibody MCA1
Components
  • MCA1 heavy chain
  • MCA1 light chain
  • S protein
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


membrane fusion / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / endocytosis involved in viral entry into host cell / 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
ubp-family deubiquitinating enzyme fold - #30 / Spike protein, C-terminal core receptor binding subdomain / ubp-family deubiquitinating enzyme fold / 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 / Single Sheet / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal ...ubp-family deubiquitinating enzyme fold - #30 / Spike protein, C-terminal core receptor binding subdomain / ubp-family deubiquitinating enzyme fold / 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 / Single Sheet / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, N-terminal domain superfamily / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Spike glycoprotein, betacoronavirus / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike (S) protein S1 subunit, receptor-binding domain, 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 superfamily, coronavirus / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2 / Alpha-Beta Plaits / Immunoglobulins / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Spike glycoprotein / Spike glycoprotein
Similarity search - Component
Biological speciesMiddle East respiratory syndrome coronavirus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.703 Å
AuthorsChen, C. / Wang, J.M. / Zou, T.T. / Gao, X.P. / Cui, S. / Jin, Q.
CitationJournal: J. Infect. Dis. / Year: 2017
Title: Human Neutralizing Monoclonal Antibody Inhibition of Middle East Respiratory Syndrome Coronavirus Replication in the Common Marmoset.
Authors: Chen, Z. / Bao, L. / Chen, C. / Zou, T. / Xue, Y. / Li, F. / Lv, Q. / Gu, S. / Gao, X. / Cui, S. / Wang, J. / Qin, C. / Jin, Q.
History
DepositionJul 15, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 31, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / 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 / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 2.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: S protein
B: MCA1 heavy chain
C: MCA1 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,7615
Polymers73,1543
Non-polymers6082
Water28816
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)153.460, 153.460, 97.494
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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Antibody , 2 types, 2 molecules BC

#2: Antibody MCA1 heavy chain


Mass: 24475.441 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Mammalian expression vector pCBio (others)
#3: Antibody MCA1 light chain


Mass: 23417.871 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Mammalian expression vector pCBio (others)

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein S protein


Mass: 25260.484 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 367-588
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Middle East respiratory syndrome coronavirus
Production host: Insect cell expression vector pTIE1 (others)
References: UniProt: V5RDT9, UniProt: K9N5Q8*PLUS
#4: Polysaccharide alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 545.490 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpa1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-2-2/a4-b1_b3-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}}}LINUCSPDB-CARE

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Non-polymers , 2 types, 17 molecules

#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 4.53 Å3/Da / Density % sol: 72.85 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.06 M Citric acid, 0.04 M Bis-tris propane, 16% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 30, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.703→40.33 Å / Num. obs: 36296 / % possible obs: 99.33 % / Redundancy: 6.8 % / Net I/σ(I): 9.9
Reflection shellResolution: 2.703→3.17 Å

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-2000data collection
Cootmodel building
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DO2

5do2


Resolution: 2.703→40.33 Å / SU ML: 0.44 / Cross valid method: NONE / σ(F): 1.35 / Phase error: 31.15
RfactorNum. reflection% reflection
Rfree0.2846 1733 4.78 %
Rwork0.2392 --
obs0.2414 36287 99.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.703→40.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4876 0 55 16 4947
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115051
X-RAY DIFFRACTIONf_angle_d1.1616880
X-RAY DIFFRACTIONf_dihedral_angle_d16.5743046
X-RAY DIFFRACTIONf_chiral_restr0.067793
X-RAY DIFFRACTIONf_plane_restr0.007868
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7027-2.78230.37961270.32412882X-RAY DIFFRACTION100
2.7823-2.8720.36481490.31882840X-RAY DIFFRACTION100
2.872-2.97470.40671380.31182872X-RAY DIFFRACTION100
2.9747-3.09370.39131230.31462878X-RAY DIFFRACTION100
3.0937-3.23450.35381560.29752866X-RAY DIFFRACTION100
3.2345-3.40490.33311710.28182847X-RAY DIFFRACTION100
3.4049-3.61810.30981310.26952893X-RAY DIFFRACTION100
3.6181-3.89720.27611410.24662874X-RAY DIFFRACTION100
3.8972-4.2890.26771440.21272916X-RAY DIFFRACTION100
4.289-4.90870.22771520.18312881X-RAY DIFFRACTION99
4.9087-6.18090.2281570.20552894X-RAY DIFFRACTION99
6.1809-40.33620.26231440.21182911X-RAY DIFFRACTION96

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