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- PDB-7b0b: Fab HbnC3t1p1_C6 bound to SARS-CoV-2 RBD -

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Basic information

Entry
Database: PDB / ID: 7b0b
TitleFab HbnC3t1p1_C6 bound to SARS-CoV-2 RBD
Components
  • Fab heavy chainFragment antigen-binding
  • IGK@ protein
  • Surface glycoprotein
KeywordsANTIVIRAL PROTEIN / SARS-CoV-2 / Neutralizing monoclonal antibody / receptor-binding motif / 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 / membrane => GO:0016020 / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / host cell plasma membrane / virion membrane / extracellular region
Similarity search - Function
Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulin subtype / Immunoglobulin / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain ...Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulin subtype / Immunoglobulin / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / 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 / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Spike glycoprotein / IGK@ protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Severe acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.98 Å
AuthorsBorenstein-Katz, A. / Diskin, R.
CitationJournal: Immunity / Year: 2023
Title: Somatic hypermutation introduces bystander mutations that prepare SARS-CoV-2 antibodies for emerging variants.
Authors: Korenkov, M. / Zehner, M. / Cohen-Dvashi, H. / Borenstein-Katz, A. / Kottege, L. / Janicki, H. / Vanshylla, K. / Weber, T. / Gruell, H. / Koch, M. / Diskin, R. / Kreer, C. / Klein, F.
History
DepositionNov 19, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 1, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 27, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 31, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: IGK@ protein
H: Fab heavy chain
F: Surface glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,4524
Polymers74,0283
Non-polymers4241
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5090 Å2
ΔGint-30 kcal/mol
Surface area29510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.413, 109.109, 168.170
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody IGK@ protein


Mass: 23432.926 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGK@ / Production host: Homo sapiens (human) / References: UniProt: Q6PIL8
#2: Antibody Fab heavy chain / Fragment antigen-binding


Mass: 24643.709 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Protein Surface glycoprotein


Mass: 25951.219 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Production host: Homo sapiens (human) / References: UniProt: A0A6M5SXU3
#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
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: 5.23 Å3/Da / Density % sol: 76.49 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.1M Tris pH8.5, 20% poly ethylene glycol 6000 using 14 mg/ml protein in a 1.3:1 protein to reservoir ratio

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 10, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.98→39.36 Å / Num. obs: 25113 / % possible obs: 77.27 % / Redundancy: 7 % / Rrim(I) all: 0.163 / Net I/σ(I): 4.1
Reflection shellResolution: 2.98→3.08 Å / Num. unique obs: 537 / CC1/2: 0.564

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Processing

Software
NameVersionClassification
PHENIXdev_3965refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7BZ5, Fb C6

7bz5


Resolution: 2.98→39.36 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2462 1998 7.96 %
Rwork0.209 23097 -
obs0.212 25095 77.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 159.02 Å2 / Biso mean: 60.1225 Å2 / Biso min: 15.82 Å2
Refinement stepCycle: final / Resolution: 2.98→39.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4830 0 28 0 4858
Biso mean--112.32 --
Num. residues----628
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.98-3.050.4123260.420930032614
3.05-3.140.3875520.344660866029
3.14-3.230.3682780.317689797544
3.23-3.330.33241020.29711168127056
3.33-3.450.34651220.27331416153867
3.45-3.590.3141470.26941703185081
3.59-3.750.31271690.25351950211992
3.75-3.950.26261800.22762073225398
3.95-4.20.2351820.19752111229399
4.2-4.520.21251830.167821072290100
4.52-4.970.2131860.160321602346100
4.98-5.690.18361860.16821462332100
5.69-7.160.24121880.204221792367100
7.17-39.360.2151970.19742279247699
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)
10.04740.1507-0.03420.4827-0.10870.0243-0.29440.15270.2158-0.28270.18520.1103-0.1462-0.103-0.00630.24450.00440.00630.5546-0.08910.318-4.007832.1987-14.0526
20.072-0.13580.22340.5279-0.61350.8391-0.10910.2085-0.06310.1191-0.0495-0.19250.16110.2773-0.48250.1399-0.02220.02230.2784-0.12320.23880.192323.4117-10.2439
30.05120.0943-0.02850.2006-0.05480.0343-0.03630.39860.0026-0.09980.1227-0.0039-0.0889-0.02350.07350.20560.0780.02850.4769-0.03550.1902-9.295425.1656-18.3046
40.0015-0.00280.00460.0071-0.01020.01250.0044-0.0418-0.1317-0.08960.11610.16060.1184-0.07040.00010.6736-0.058-0.1280.4433-0.02360.4563-35.85927.5811-34.6994
50.41340.06-0.04570.1067-0.06460.16690.0730.25790.1022-0.14810.0285-0.0294-0.05040.1508-0.00550.295-0.04150.00520.3488-0.10070.2098-27.273619.0654-35.6914
60.05450.00970.01460.05280.03880.16820.00440.0213-0.0464-0.0375-0.07710.23630.1561-0.0507-0.35710.18020.0529-0.01820.0363-0.07610.3539-16.8478.456-0.5622
70.1143-0.0547-0.2430.13360.18220.55380.0459-0.0038-0.03480.0951-0.0788-0.0610.0061-0.09370.00230.1997-0.032-0.0650.12550.04120.3024-22.674412.06143.2776
80.1890.0862-0.05160.0722-0.10160.17870.09070.0446-0.2085-0.00650.181-0.1069-0.1493-0.04840.05350.17850.0272-0.01430.34670.01850.1823-13.751621.58563.5114
90.7683-0.275-0.26160.4936-0.30470.4934-0.0505-0.2348-0.08450.142-0.2097-0.1050.02790.0108-0.37460.05180.0127-0.05710.41980.05810.3828-18.847716.35749.8526
100.12180.0643-0.15050.4117-0.41340.4856-0.0864-0.041-0.0903-0.0518-0.101-0.12050.18650.4451-0.82010.12870.063-0.03870.3522-0.12470.2416-20.002112.8763-10.7877
110.0474-0.04320.00530.2181-0.0790.03110.00440.0862-0.1132-0.0820.0282-0.06060.25280.03610.10790.38820.0346-0.0450.3661-0.24670.3417-23.86882.3053-20.8848
120.0765-0.03980.02190.28420.06530.02730.09440.1283-0.204-0.00070.0831-0.08820.49930.07430.75530.534-0.01780.03250.1564-0.17120.2938-25.19712.7983-28.0719
130.0909-0.0799-0.08270.06680.07120.0765-0.0275-0.03120.07540.47270.16430.2555-0.2940.09040.02960.7648-0.00340.05710.52730.0470.2703-6.819523.742150.5057
140.2860.11240.02920.47640.2050.0913-0.1273-0.091-0.03170.0133-0.03950.04550.01890.1983-0.2170.94950.0831-0.13860.55110.32240.5927-3.573711.617753.2185
150.28450.17140.05120.17940.06950.14760.1914-0.3403-0.54460.26270.0880.16840.43920.06590.03950.46010.1556-0.03650.4160.12840.4134-5.41416.042338.4528
160.45790.0448-0.02090.71150.45720.30.00490.14890.0497-0.13660.1259-0.0559-0.02830.18810.18860.28350.03310.07640.63080.19310.2558-10.771824.300327.6354
170.0431-0.0229-0.08190.675-0.08050.17370.09480.16720.1590.1935-0.0465-0.19660.02390.25550.02880.2028-0.0721-0.13330.53530.06130.33270.093826.449320.9535
180.71380.08350.57480.03130.0820.58370.20610.20470.06610.0670.00850.15340.0709-0.04720.06140.3911-0.12340.04210.75390.24370.3898-13.685517.769437.3497
190.0384-0.0131-0.02330.00460.00770.01620.0427-0.0372-0.08020.05880.11470.0027-0.12650.05910.00081.14780.0236-0.06211.2811-0.10590.94648.681521.720758.0618
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'L' and (resid 1 through 30 )L1 - 30
2X-RAY DIFFRACTION2chain 'L' and (resid 31 through 91 )L31 - 91
3X-RAY DIFFRACTION3chain 'L' and (resid 92 through 116 )L92 - 116
4X-RAY DIFFRACTION4chain 'L' and (resid 117 through 129 )L117 - 129
5X-RAY DIFFRACTION5chain 'L' and (resid 130 through 215 )L130 - 215
6X-RAY DIFFRACTION6chain 'H' and (resid 2 through 12 )H2 - 12
7X-RAY DIFFRACTION7chain 'H' and (resid 13 through 25 )H13 - 25
8X-RAY DIFFRACTION8chain 'H' and (resid 26 through 64 )H26 - 64
9X-RAY DIFFRACTION9chain 'H' and (resid 65 through 83 )H65 - 83
10X-RAY DIFFRACTION10chain 'H' and (resid 84 through 155 )H84 - 155
11X-RAY DIFFRACTION11chain 'H' and (resid 156 through 167 )H156 - 167
12X-RAY DIFFRACTION12chain 'H' and (resid 168 through 224 )H168 - 224
13X-RAY DIFFRACTION13chain 'F' and (resid 333 through 371 )F333 - 371
14X-RAY DIFFRACTION14chain 'F' and (resid 372 through 393 )F372 - 393
15X-RAY DIFFRACTION15chain 'F' and (resid 394 through 442 )F394 - 442
16X-RAY DIFFRACTION16chain 'F' and (resid 443 through 459 )F443 - 459
17X-RAY DIFFRACTION17chain 'F' and (resid 460 through 494 )F460 - 494
18X-RAY DIFFRACTION18chain 'F' and (resid 495 through 516 )F495 - 516
19X-RAY DIFFRACTION19chain 'F' and (resid 517 through 526 )F517 - 526

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