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- PDB-6zlr: Soaking competent crystal form of the SARS-CoV-2 Receptor Binding... -

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Basic information

Entry
Database: PDB / ID: 6zlr
TitleSoaking competent crystal form of the SARS-CoV-2 Receptor Binding Domain (RBD):CR3022 complex.
Components
  • CR3022 FAB HEAVY CHAIN
  • CR3022 FAB LIGHT CHAIN
  • Spike glycoprotein
KeywordsVIRAL PROTEIN / SARS-COV-2 / VIRAL PROTEIN COMPLEX / ANTIBODY
Function / homology
Function and homology information


symbiont-mediated disruption of host tissue / Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / viral translation / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion ...symbiont-mediated disruption of host tissue / Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / viral translation / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell / membrane fusion / Attachment and Entry / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / host cell surface receptor binding / symbiont-mediated suppression of host innate immune response / receptor ligand activity / 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 / symbiont entry into host cell / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / identical protein binding / membrane / plasma membrane
Similarity search - Function
Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / 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 ...Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / 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
Similarity search - Domain/homology
Biological speciesSevere acute respiratory syndrome coronavirus 2
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
Authorsde Nicola, G.F. / Nichols, C.E.
CitationJournal: Front Pharmacol / Year: 2020
Title: A New Crystal Form of the SARS-CoV-2 Receptor Binding Domain: CR3022 Complex-An Ideal Target for In-Crystal Fragment Screening of the ACE2 Binding Site Surface.
Authors: Nichols, C. / Ng, J. / Keshu, A. / Fraternali, F. / De Nicola, G.F.
History
DepositionJul 1, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 23, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 13, 2021Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 31, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
EEE: Spike glycoprotein
HHH: CR3022 FAB HEAVY CHAIN
LLL: CR3022 FAB LIGHT CHAIN
AAA: Spike glycoprotein
BBB: CR3022 FAB HEAVY CHAIN
CCC: CR3022 FAB LIGHT CHAIN
DDD: Spike glycoprotein
FFF: CR3022 FAB HEAVY CHAIN
GGG: CR3022 FAB LIGHT CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)222,44712
Polymers221,7839
Non-polymers6643
Water00
1
EEE: Spike glycoprotein
HHH: CR3022 FAB HEAVY CHAIN
LLL: CR3022 FAB LIGHT CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,1494
Polymers73,9283
Non-polymers2211
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5840 Å2
ΔGint-32 kcal/mol
Surface area28560 Å2
MethodPISA
2
AAA: Spike glycoprotein
BBB: CR3022 FAB HEAVY CHAIN
CCC: CR3022 FAB LIGHT CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,1494
Polymers73,9283
Non-polymers2211
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5860 Å2
ΔGint-33 kcal/mol
Surface area28460 Å2
MethodPISA
3
DDD: Spike glycoprotein
FFF: CR3022 FAB HEAVY CHAIN
GGG: CR3022 FAB LIGHT CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,1494
Polymers73,9283
Non-polymers2211
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5800 Å2
ΔGint-31 kcal/mol
Surface area28640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)207.130, 207.130, 199.866
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11Chains E A
22Chains E D
33Chains H B
44Chains H F
55Chains L C
66Chains L G
77Chains A D
88Chains B F
99Chains C G

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9

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Components

#1: Protein Spike glycoprotein / S glycoprotein / E2 / Peplomer protein


Mass: 26095.348 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: S, 2 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P0DTC2
#2: Antibody CR3022 FAB HEAVY CHAIN


Mass: 23455.420 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody CR3022 FAB LIGHT CHAIN


Mass: 24376.963 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
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
Has ligand of interestN
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: 5.13 Å3/Da / Density % sol: 76.02 % / Description: Thin Rod
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.7
Details: 0.1 M SODIUM MALONATE, 0.1 M TRIS PH 7.7, 22% W/V POLYETHYLENE GLYCOL 1,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9999 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 20, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 3.09→68.028 Å / Num. obs: 72060 / % possible obs: 91.1 % / Redundancy: 4.7 % / CC1/2: 0.933 / Net I/σ(I): 4.6
Reflection shellResolution: 3.09→3.16 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 4356 / CC1/2: 0.415 / % possible all: 90.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6W41

6w41


Resolution: 3.1→68.028 Å / Cor.coef. Fo:Fc: 0.907 / Cor.coef. Fo:Fc free: 0.885 / SU B: 19.006 / SU ML: 0.303 / Cross valid method: FREE R-VALUE / ESU R: 0.908 / ESU R Free: 0.375
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2472 3669 5.123 %
Rwork0.2176 67946 -
all0.219 --
obs-71615 90.525 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 55.64 Å2
Baniso -1Baniso -2Baniso -3
1-0.063 Å2-0 Å20 Å2
2--0.063 Å20 Å2
3----0.125 Å2
Refinement stepCycle: LAST / Resolution: 3.1→68.028 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14694 0 42 0 14736
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01315134
X-RAY DIFFRACTIONr_bond_other_d0.0010.01713355
X-RAY DIFFRACTIONr_angle_refined_deg1.5481.6520619
X-RAY DIFFRACTIONr_angle_other_deg1.2271.57331205
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.62251902
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.09923.393672
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.873152364
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.111551
X-RAY DIFFRACTIONr_chiral_restr0.0570.21986
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216981
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023130
X-RAY DIFFRACTIONr_nbd_refined0.1830.22181
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1890.212015
X-RAY DIFFRACTIONr_nbtor_refined0.1690.27262
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.26876
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1850.2217
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.210.28
X-RAY DIFFRACTIONr_nbd_other0.1920.250
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1870.22
X-RAY DIFFRACTIONr_mcbond_it4.9925.8717635
X-RAY DIFFRACTIONr_mcbond_other4.9925.877634
X-RAY DIFFRACTIONr_mcangle_it8.0478.7929528
X-RAY DIFFRACTIONr_mcangle_other8.0478.7939529
X-RAY DIFFRACTIONr_scbond_it5.1536.2247499
X-RAY DIFFRACTIONr_scbond_other5.1496.2237497
X-RAY DIFFRACTIONr_scangle_it8.2439.15711091
X-RAY DIFFRACTIONr_scangle_other8.2439.15711091
X-RAY DIFFRACTIONr_lrange_it13.544110.05759019
X-RAY DIFFRACTIONr_lrange_other13.544110.05659019
X-RAY DIFFRACTIONr_ncsr_local_group_10.0250.056128
X-RAY DIFFRACTIONr_ncsr_local_group_20.0230.056134
X-RAY DIFFRACTIONr_ncsr_local_group_30.0230.056545
X-RAY DIFFRACTIONr_ncsr_local_group_40.0290.056557
X-RAY DIFFRACTIONr_ncsr_local_group_50.0310.056804
X-RAY DIFFRACTIONr_ncsr_local_group_60.0270.056770
X-RAY DIFFRACTIONr_ncsr_local_group_70.0240.056153
X-RAY DIFFRACTIONr_ncsr_local_group_80.030.056544
X-RAY DIFFRACTIONr_ncsr_local_group_90.0390.056757
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.180.3572910.355035X-RAY DIFFRACTION92.0498
3.18-3.2680.3452390.3194921X-RAY DIFFRACTION91.995
3.268-3.3620.3342570.2994791X-RAY DIFFRACTION92.0664
3.362-3.4660.3072620.2834616X-RAY DIFFRACTION91.8471
3.466-3.5790.3062580.2644498X-RAY DIFFRACTION91.8679
3.579-3.7050.2722660.2464323X-RAY DIFFRACTION91.6883
3.705-3.8450.2821950.234196X-RAY DIFFRACTION91.0052
3.845-4.0010.2521990.2184045X-RAY DIFFRACTION91.1121
4.001-4.1790.2642090.213836X-RAY DIFFRACTION90.8172
4.179-4.3830.1972050.1823671X-RAY DIFFRACTION90.6879
4.383-4.620.1891730.1593529X-RAY DIFFRACTION90.5135
4.62-4.90.1671670.163326X-RAY DIFFRACTION90.422
4.9-5.2380.2111500.1623124X-RAY DIFFRACTION89.6004
5.238-5.6570.181580.1722864X-RAY DIFFRACTION88.804
5.657-6.1960.221590.1762614X-RAY DIFFRACTION88.2559
6.196-6.9260.1941200.1612406X-RAY DIFFRACTION87.7083
6.926-7.9940.1871410.1642111X-RAY DIFFRACTION88.0375
7.994-9.7830.2161060.1741789X-RAY DIFFRACTION87.4078
9.783-13.8050.237820.2071423X-RAY DIFFRACTION86.5938
13.805-68.0280.36320.325828X-RAY DIFFRACTION83.2527

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