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- PDB-8cwi: Fab arm of antibody 10G4 bound to CoV-2 receptor binding domain (RBD) -

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Basic information

Entry
Database: PDB / ID: 8cwi
TitleFab arm of antibody 10G4 bound to CoV-2 receptor binding domain (RBD)
Components
  • Heavy chain of Fab arm of antibody 10G4
  • Light chain of Fab arm of antibody 10G4
  • Spike protein S1
KeywordsIMMUNE SYSTEM / antibody / CoV-2 / receptor binding domain / class 5 epitope
Function / homology
Function and homology information


Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell ...Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated endocytosis of virus by host cell / membrane fusion / Attachment and Entry / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / 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 / 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 ...Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / 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
Biological speciesSevere acute respiratory syndrome coronavirus 2
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.873 Å
AuthorsLangley, D.B. / Christ, D.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia) Australia
CitationJournal: To Be Published
Title: Neutralization of CoV-2 omicron lineages by affinity-matured class 5 antibodies
Authors: Langley, D.B. / Christ, D.
History
DepositionMay 19, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 24, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Spike protein S1
H: Heavy chain of Fab arm of antibody 10G4
L: Light chain of Fab arm of antibody 10G4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,82510
Polymers71,0423
Non-polymers1,7827
Water12,016667
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7240 Å2
ΔGint-44 kcal/mol
Surface area29460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.691, 88.639, 81.398
Angle α, β, γ (deg.)90.000, 95.030, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Spike protein S1


Mass: 22975.688 Da / Num. of mol.: 1 / Fragment: receptor binding domain (RBD)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: S, 2 / Cell line (production host): ExpiCHO / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P0DTC2

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Antibody , 2 types, 2 molecules HL

#2: Antibody Heavy chain of Fab arm of antibody 10G4


Mass: 24475.314 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): ExpiCHO / Production host: Cricetulus griseus (Chinese hamster)
#3: Antibody Light chain of Fab arm of antibody 10G4


Mass: 23591.232 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): ExpiCHO / Production host: Cricetulus griseus (Chinese hamster)

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Sugars , 2 types, 2 molecules

#4: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1056.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3-3-4/a4-b1_a6-f1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#5: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE

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Non-polymers , 3 types, 672 molecules

#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 667 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.72 Å3/Da / Density % sol: 54.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: Equal volumes (0.4 uL) of protein solution (~5 mg/mL in 25 mM Tris (pH 8.0), 200 mM NaCl) were combined with well solution (200 mM MgCl2, 100 mM sodium acetate (pH 5.0), 20 % (w/v) PEG6000) ...Details: Equal volumes (0.4 uL) of protein solution (~5 mg/mL in 25 mM Tris (pH 8.0), 200 mM NaCl) were combined with well solution (200 mM MgCl2, 100 mM sodium acetate (pH 5.0), 20 % (w/v) PEG6000) in a sitting drop format.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953651 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 21, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953651 Å / Relative weight: 1
ReflectionResolution: 1.87→46.562 Å / Num. obs: 61471 / % possible obs: 98.5 % / Redundancy: 7.1 % / Biso Wilson estimate: 27.19 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.03 / Rrim(I) all: 0.079 / Net I/σ(I): 14.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.87-1.927.20.7512794738720.8620.2970.8082.596.3
8.98-46.566.90.02840675930.9990.0110.0350.899.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.68 Å46.56 Å
Translation3.68 Å46.56 Å

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
XDSdata reduction
Aimless0.7.4data scaling
PHASER2.8.3phasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: generic fab and RBD

Resolution: 1.873→46.562 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2049 3038 4.94 %
Rwork0.1699 58401 -
obs0.1716 61439 98.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 106.67 Å2 / Biso mean: 35.1822 Å2 / Biso min: 16.67 Å2
Refinement stepCycle: final / Resolution: 1.873→46.562 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4797 0 114 667 5578
Biso mean--67.06 42.32 -
Num. residues----627
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065144
X-RAY DIFFRACTIONf_angle_d0.8517043
X-RAY DIFFRACTIONf_chiral_restr0.053796
X-RAY DIFFRACTIONf_plane_restr0.005901
X-RAY DIFFRACTIONf_dihedral_angle_d8.4244061
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.8732-1.90250.2661190.2424257196
1.9025-1.93370.22561660.2242261598
1.9337-1.9670.2731210.2066259798
1.967-2.00280.24241350.1975265198
2.0028-2.04130.25561310.1926263298
2.0413-2.0830.23551330.1929264898
2.083-2.12830.2511320.1916260398
2.1283-2.17780.23171210.1855266898
2.1778-2.23220.23771530.1813262498
2.2322-2.29260.24531420.1773263398
2.2926-2.360.18951400.1803266998
2.36-2.43620.22261350.1819264398
2.4362-2.52330.24881580.178265298
2.5233-2.62430.22031380.1805263199
2.6243-2.74370.2581470.1832267899
2.7437-2.88840.21811370.1906265299
2.8884-3.06930.23641190.1832270899
3.0693-3.30620.2221360.1797268099
3.3062-3.63880.19951470.1653268199
3.6388-4.16510.18241510.1476268799
4.1651-5.24640.15011290.12392717100
5.2464-46.5620.15431480.1649276199
Refinement TLS params.Method: refined / Origin x: -19.2869 Å / Origin y: 37.119 Å / Origin z: 21.3969 Å
111213212223313233
T0.2319 Å2-0.0177 Å2-0.0228 Å2-0.1714 Å20.0019 Å2--0.175 Å2
L0.3338 °2-0.2387 °20.0242 °2-0.4751 °20.0765 °2--0.1956 °2
S0.0128 Å °0.0474 Å °0.014 Å °-0.0458 Å °-0.0396 Å °0.0307 Å °-0.0486 Å °-0.0148 Å °0.0251 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA334 - 528
2X-RAY DIFFRACTION1allA529 - 532
3X-RAY DIFFRACTION1allA533 - 534
4X-RAY DIFFRACTION1allH1 - 218
5X-RAY DIFFRACTION1allL1 - 225
6X-RAY DIFFRACTION1allL226
7X-RAY DIFFRACTION1allB1 - 2
8X-RAY DIFFRACTION1allC1
9X-RAY DIFFRACTION1allC2
10X-RAY DIFFRACTION1allC3
11X-RAY DIFFRACTION1allS1 - 687

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