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- PDB-8cwj: Fab arms of antibodies 4C12-B12 and CR3022 bound to pangolin rece... -

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Basic information

Entry
Database: PDB / ID: 8cwj
TitleFab arms of antibodies 4C12-B12 and CR3022 bound to pangolin receptor binding domain (pRBD)
Components
  • (Heavy chain of ...) x 2
  • (Light chain of ...) x 2
  • Spike glycoprotein
KeywordsIMMUNE SYSTEM / antibody / pangolin / receptor binding domain / class 5 epitope
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
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 speciesHomo sapiens (human)
Pangolin coronavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.449 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
H: Heavy chain of CR3022 antibody Fab
L: Light chain of CR3022 antibody Fab
G: Spike glycoprotein
A: Heavy chain of CR3022 antibody Fab
B: Light chain of CR3022 antibody Fab
I: Spike glycoprotein
J: Heavy chain of 4C12-B12 antibody Fab
K: Light chain of 4C12-B12 antibody Fab
U: Heavy chain of 4C12-B12 antibody Fab
V: Light chain of 4C12-B12 antibody Fab
hetero molecules


Theoretical massNumber of molelcules
Total (without water)242,84939
Polymers239,18010
Non-polymers3,66929
Water6,539363
1
H: Heavy chain of CR3022 antibody Fab
L: Light chain of CR3022 antibody Fab
G: Spike glycoprotein
J: Heavy chain of 4C12-B12 antibody Fab
K: Light chain of 4C12-B12 antibody Fab
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,11218
Polymers119,5905
Non-polymers1,52213
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Heavy chain of CR3022 antibody Fab
B: Light chain of CR3022 antibody Fab
I: Spike glycoprotein
U: Heavy chain of 4C12-B12 antibody Fab
V: Light chain of 4C12-B12 antibody Fab
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,73721
Polymers119,5905
Non-polymers2,14716
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)157.433, 144.097, 168.842
Angle α, β, γ (deg.)90.000, 117.510, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 2 molecules GI

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


Mass: 22891.547 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pangolin coronavirus / Cell line (production host): ExpiCHO / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: A0A7D6TQ96

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Antibody , 4 types, 8 molecules HALBJUKV

#1: Antibody Heavy chain of CR3022 antibody Fab


Mass: 24428.432 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): ExpCHO / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody Light chain of CR3022 antibody Fab


Mass: 24289.885 Da / Num. of mol.: 2
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)
#4: Antibody Heavy chain of 4C12-B12 antibody Fab


Mass: 24514.238 Da / Num. of mol.: 2
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)
#5: Antibody Light chain of 4C12-B12 antibody Fab


Mass: 23466.057 Da / Num. of mol.: 2
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, 4 molecules

#6: 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.: 3
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
#8: 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.: 1 / Source method: obtained synthetically / 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 , 3 types, 388 molecules

#7: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C3H8O3
#9: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Cl
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 363 / 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: 3.55 Å3/Da / Density % sol: 65.32 % / Description: tiles
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: Equal volumes of protein complex (1:1:1 molar ratio, at ~ 5 mg/mL, in 25 mM Tris (pH 8.0), 200 mM NaCl) were combined with well solution (200 mM sodium citrate (pH 5.6), 12% (w/v) PEG6000).

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9536 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 23, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9536 Å / Relative weight: 1
ReflectionResolution: 2.449→48.69 Å / Num. obs: 122620 / % possible obs: 100 % / Redundancy: 7 % / Biso Wilson estimate: 55.09 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.044 / Rrim(I) all: 0.119 / Net I/σ(I): 11.8
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
2.45-2.497.21.1514403860800.7730.4571.2391.4100
13.41-48.696.80.04151707650.9980.0170.04442.797.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.45 Å48.69 Å
Translation2.45 Å48.69 Å

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Processing

Software
NameVersionClassification
PHENIX1.11.1refinement
XDSdata reduction
Aimless0.7.7data scaling
PHASER2.8.3phasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: generic RBD and Fab

Resolution: 2.449→48.69 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 27.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2301 6036 4.92 %
Rwork0.1962 116534 -
obs0.1979 122570 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 168.95 Å2 / Biso mean: 70.3295 Å2 / Biso min: 28.27 Å2
Refinement stepCycle: final / Resolution: 2.449→48.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16063 0 228 363 16654
Biso mean--111.79 56.29 -
Num. residues----2121
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00216863
X-RAY DIFFRACTIONf_angle_d0.6423023
X-RAY DIFFRACTIONf_chiral_restr0.0462582
X-RAY DIFFRACTIONf_plane_restr0.0042953
X-RAY DIFFRACTIONf_dihedral_angle_d14.6119982
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.449-2.47680.34981720.33273921
2.4768-2.5060.40591890.31593831
2.506-2.53650.37881970.3183912
2.5365-2.56860.34322080.29333846
2.5686-2.60240.31942020.28453895
2.6024-2.63810.31942100.27043827
2.6381-2.67580.30361960.25913902
2.6758-2.71570.32122030.25733885
2.7157-2.75810.31042180.25893805
2.7581-2.80340.30832070.25313888
2.8034-2.85170.28161920.24763845
2.8517-2.90350.26912090.24643884
2.9035-2.95940.26442280.23943885
2.9594-3.01980.29642150.24693856
3.0198-3.08540.30122000.25573862
3.0854-3.15720.2671720.23223897
3.1572-3.23610.26591670.23433924
3.2361-3.32360.30872050.23043906
3.3236-3.42140.23171810.21363892
3.4214-3.53180.24062070.20583882
3.5318-3.6580.23431960.19463856
3.658-3.80440.22622160.19793884
3.8044-3.97740.22671900.18663908
3.9774-4.1870.1951990.16783880
4.187-4.44920.17711970.14423913
4.4492-4.79250.17371960.14253885
4.7925-5.27420.17442080.14273897
5.2742-6.03620.20481850.16153941
6.0362-7.60030.21872300.17343900
7.6003-48.690.17692410.17213925
Refinement TLS params.Method: refined / Origin x: 41.9371 Å / Origin y: 2.277 Å / Origin z: 39.4967 Å
111213212223313233
T0.3887 Å20.0326 Å20.0076 Å2-0.3814 Å2-0.0165 Å2--0.2807 Å2
L0.4456 °2-0.1669 °20.1127 °2-0.4154 °20.0099 °2--0.5095 °2
S0.0218 Å °0.066 Å °-0.0484 Å °-0.0488 Å °-0.0064 Å °0.0127 Å °-0.079 Å °0.075 Å °-0.013 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allH1 - 220
2X-RAY DIFFRACTION1allH301
3X-RAY DIFFRACTION1allL1 - 220
4X-RAY DIFFRACTION1allG333 - 529
5X-RAY DIFFRACTION1allG530 - 533
6X-RAY DIFFRACTION1allG536
7X-RAY DIFFRACTION1allG537 - 539
8X-RAY DIFFRACTION1allA1 - 222
9X-RAY DIFFRACTION1allB1 - 218
10X-RAY DIFFRACTION1allI333 - 529
11X-RAY DIFFRACTION1allI531
12X-RAY DIFFRACTION1allI532
13X-RAY DIFFRACTION1allI533 - 538
14X-RAY DIFFRACTION1allI539 - 541
15X-RAY DIFFRACTION1allI542
16X-RAY DIFFRACTION1allJ1 - 219
17X-RAY DIFFRACTION1allJ301
18X-RAY DIFFRACTION1allJ302
19X-RAY DIFFRACTION1allK1 - 214
20X-RAY DIFFRACTION1allK300
21X-RAY DIFFRACTION1allU1 - 219
22X-RAY DIFFRACTION1allU301
23X-RAY DIFFRACTION1allV1 - 300
24X-RAY DIFFRACTION1allS2 - 422
25X-RAY DIFFRACTION1allC1
26X-RAY DIFFRACTION1allC2
27X-RAY DIFFRACTION1allC3 - 12

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