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- PDB-4zs6: Receptor binding domain and Fab complex -

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Basic information

Entry
Database: PDB / ID: 4zs6
TitleReceptor binding domain and Fab complex
Components
  • S proteinCoronavirus spike protein
  • fab Heavy ChainFragment antigen-binding
  • fab Light ChainFragment antigen-binding
KeywordsIMMUNE SYSTEM / complex / Fab / Receptor binding domain
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 / 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 / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily ...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 / 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Middle East respiratory syndrome coronavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.166 Å
AuthorsYu, X. / Wang, X.
CitationJournal: Sci Rep / Year: 2015
Title: Structural basis for the neutralization of MERS-CoV by a human monoclonal antibody MERS-27
Authors: Yu, X. / Zhang, S. / Jiang, L. / Cui, Y. / Li, D. / Wang, D. / Wang, N. / Fu, L. / Shi, X. / Li, Z. / Zhang, L. / Wang, X.
History
DepositionMay 13, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 2, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_oper_list / 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 / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / 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_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: fab Light Chain
H: fab Heavy Chain
A: S protein
D: fab Light Chain
C: fab Heavy Chain
B: S protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,91410
Polymers146,0306
Non-polymers8854
Water0
1
L: fab Light Chain
H: fab Heavy Chain
A: S protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,4575
Polymers73,0153
Non-polymers4422
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: fab Light Chain
C: fab Heavy Chain
B: S protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,4575
Polymers73,0153
Non-polymers4422
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.492, 64.461, 186.049
Angle α, β, γ (deg.)90.000, 100.430, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
12chain C
22chain H
13chain D
23chain L

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11VALVALNAGNAGchain AAC - H381 - 70215
21VALVALNAGNAGchain BBF - J381 - 70215
12VALVALLYSLYSchain CCE2 - 2222 - 222
22VALVALLYSLYSchain HHB2 - 2222 - 222
13ALAALAARGARGchain DDD1 - 2101 - 210
23ALAALAARGARGchain LLA1 - 2101 - 210

NCS ensembles :
ID
1
2
3

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Components

#1: Antibody fab Light Chain / Fragment antigen-binding


Mass: 23344.000 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK 293T / Production host: Homo sapiens (human)
#2: Antibody fab Heavy Chain / Fragment antigen-binding


Mass: 24412.357 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK 293T / Production host: Homo sapiens (human)
#3: Protein S protein / Coronavirus spike protein


Mass: 25258.402 Da / Num. of mol.: 2 / Fragment: Receptor binding domain, UNP residues 361-589
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Middle East respiratory syndrome coronavirus
Cell line (production host): sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: W6A0A7
#4: 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.: 4
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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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.27 Å3/Da / Density % sol: 62.42 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M MES monohydrate (pH 6.5), 12% (w/v) Polyethylene glycol 20000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: RIGAKU SATURN A200 / Detector: CCD / Date: May 6, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3.166→50 Å / Num. obs: 31146 / % possible obs: 95.1 % / Redundancy: 5 % / Biso Wilson estimate: 71.11 Å2 / Rmerge(I) obs: 0.17 / Χ2: 1.116 / Net I/av σ(I): 8.484 / Net I/σ(I): 7.1 / Num. measured all: 156458
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
3.166-3.275.10.87621131.02196.7
3.27-3.365.20.69920571.06996.8
3.36-3.455.20.52320941.10796.5
3.45-3.555.20.40520741.16496.4
3.55-3.665.20.33520871.18896.2
3.66-3.795.20.29220691.19896.1
3.79-3.955.10.25920771.11996
3.95-4.135.10.21520881.11495.7
4.13-4.3450.16920881.0995.3
4.34-4.614.90.13520571.04395
4.61-4.974.90.12620850.98395.2
4.97-5.474.80.11920601.10493.9
5.47-6.264.90.1220451.28194
6.26-7.8850.11420781.31593.8
7.88-504.60.08520740.93390.1

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4L72

4l72


Resolution: 3.166→36.953 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.245 1565 5.03 %
Rwork0.2033 29564 -
obs0.2055 31129 94.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 137.23 Å2 / Biso mean: 68.8969 Å2 / Biso min: 32.55 Å2
Refinement stepCycle: final / Resolution: 3.166→36.953 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9786 0 56 0 9842
Biso mean--91.7 --
Num. residues----1276
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01110110
X-RAY DIFFRACTIONf_angle_d1.49413752
X-RAY DIFFRACTIONf_chiral_restr0.0561568
X-RAY DIFFRACTIONf_plane_restr0.0081750
X-RAY DIFFRACTIONf_dihedral_angle_d15.7983628
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1899X-RAY DIFFRACTION5.231TORSIONAL
12B1899X-RAY DIFFRACTION5.231TORSIONAL
21C1957X-RAY DIFFRACTION5.231TORSIONAL
22H1957X-RAY DIFFRACTION5.231TORSIONAL
31D1967X-RAY DIFFRACTION5.231TORSIONAL
32L1967X-RAY DIFFRACTION5.231TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.166-3.26820.37141420.29752576271891
3.2682-3.38490.2831360.26142745288197
3.3849-3.52030.29861590.24252658281796
3.5203-3.68040.28561260.23192723284996
3.6804-3.87420.26441330.22892734286796
3.8742-4.11670.26811310.21382690282196
4.1167-4.43410.23551650.18622664282995
4.4341-4.87940.21831280.16942737286595
4.8794-5.58330.19781480.18592643279194
5.5833-7.02650.24061410.19912712285394
7.0265-36.95560.21621560.17272682283891
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)
12.99290.4701-0.61411.0471-0.11091.3340.00080.078-0.1515-0.07190.0081-0.1213-0.28580.46950.00030.4241-0.1032-0.07520.5196-0.02840.53327.511616.6175626.5329
22.27730.9379-0.75821.038-0.63332.4997-0.05290.7940.0366-0.1240.21190.0383-0.2698-0.19520.00270.5570.0118-0.04170.52640.04070.4795-7.694817.3333615.9956
31.7562-0.2344-0.61541.78920.67383.0201-0.0064-0.17380.21240.2768-0.00510.0549-0.189-0.1804-0.00010.33390.0062-0.05740.38570.03370.494-32.485410.999657.5675
43.295-1.2123-1.47063.06291.18121.58410.26250.2459-0.2826-0.3102-0.2687-0.2092-0.1692-0.2030.00050.6554-0.01610.02460.84960.0620.5142-22.570625.5204592.7481
51.51840.0154-0.31540.51960.57252.49790.1058-0.0666-0.49050.0609-0.24040.2760.6698-0.3296-0.00041.099-0.10220.08650.4759-0.07310.88881.9963-6.6042564.7544
61.7889-0.1681-0.11761.0339-0.36710.8119-0.164-0.4923-0.0244-0.19280.0723-0.15540.17170.3683-0.00320.8493-0.0290.16010.5102-0.05940.808616.6913.9025569.3645
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain LL1 - 210
2X-RAY DIFFRACTION2chain HH2 - 222
3X-RAY DIFFRACTION3chain AA381 - 702
4X-RAY DIFFRACTION4chain BB381 - 702
5X-RAY DIFFRACTION5chain CC2 - 222
6X-RAY DIFFRACTION6chain DD1 - 210

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