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- PDB-8sis: Crystal structure of SARS-CoV-2 spike receptor-binding domain in ... -

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Basic information

Entry
Database: PDB / ID: 8sis
TitleCrystal structure of SARS-CoV-2 spike receptor-binding domain in complex with broadly neutralizing antibody CC84.2 Fab
Components
  • CC84.2 Fab heavy chain
  • CC84.2 Fab light chain
  • Spike protein S1
KeywordsIMMUNE SYSTEM / bnAb / SARS-CoV-2 / broadly neutralizing antibody / spike / RBD
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 / Resolution: 3.08 Å
AuthorsLiu, H. / Wilson, I.A.
Funding support United States, 1items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationINV-004923 United States
CitationJournal: Biorxiv / Year: 2023
Title: Broadly neutralizing antibodies targeting a conserved silent face of spike RBD resist extreme SARS-CoV-2 antigenic drift
Authors: Song, G. / Yuan, M. / Liu, H. / Capozzola, T. / Lin, R. / Torres, J. / He, W. / Musharrafieh, R. / Dueker, K. / Zhou, P. / Callaghan, S. / Mishra, N. / Yong, P. / Anzanello, F. / Avillion, G. ...Authors: Song, G. / Yuan, M. / Liu, H. / Capozzola, T. / Lin, R. / Torres, J. / He, W. / Musharrafieh, R. / Dueker, K. / Zhou, P. / Callaghan, S. / Mishra, N. / Yong, P. / Anzanello, F. / Avillion, G. / Vo, A. / Li, X. / Makhdoomi, M. / Feng, Z. / Zhu, X. / Peng, L. / Nemazee, D. / Safonova, Y. / Briney, B. / Ward, A. / Burton, D. / Wilson, I. / Andrabi, R.
History
DepositionApr 16, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Spike protein S1
H: CC84.2 Fab heavy chain
L: CC84.2 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,8624
Polymers71,6413
Non-polymers2211
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.698, 80.188, 73.537
Angle α, β, γ (deg.)90.00, 94.90, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Spike protein S1


Mass: 23104.867 Da / Num. of mol.: 1 / Fragment: Receptor binding domain, UNP residues 333-530
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P0DTC2
#2: Antibody CC84.2 Fab heavy chain


Mass: 24965.904 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Mus musculus (house mouse)
#3: Antibody CC84.2 Fab light chain


Mass: 23570.090 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Mus musculus (house mouse)
#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.: 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
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: 2.82 Å3/Da / Density % sol: 56.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20% (w/v) PEG 3000, 0.1 M Sodium citrate pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03317 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Oct 8, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03317 Å / Relative weight: 1
ReflectionResolution: 3.08→50 Å / Num. obs: 14522 / % possible obs: 97.9 % / Redundancy: 4.2 % / CC1/2: 0.992 / CC star: 0.998 / Rmerge(I) obs: 0.205 / Rpim(I) all: 0.112 / Rrim(I) all: 0.234 / Χ2: 0.936 / Net I/σ(I): 4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
3.1-3.154.21.1817060.7170.9140.6361.3460.8897
3.15-3.214.11.1417340.730.9190.6211.3050.86498.5
3.21-3.274.10.9347090.8370.9550.5131.070.89698.3
3.27-3.344.10.7577280.8530.960.4140.8670.85298.4
3.34-3.413.90.6347150.8390.9550.3610.7340.93997.4
3.41-3.493.90.5686750.8930.9710.3230.6570.93291.3
3.49-3.584.30.5347410.9070.9750.2860.6070.91299.5
3.58-3.684.50.4397340.9480.9870.2330.4980.93399.1
3.68-3.784.40.4287200.9290.9810.2270.4860.98599
3.78-3.914.40.3547390.9390.9840.1880.4020.94699.3
3.91-4.044.40.2987370.9460.9860.160.3390.9899.3
4.04-4.214.30.2397300.9590.990.1280.2721.07799.2
4.21-4.44.20.1937240.970.9920.1050.2211.01799
4.4-4.634.20.1647390.9750.9940.0920.1891.06498.3
4.63-4.9240.1517290.9770.9940.0850.1741.07697.9
4.92-5.340.1466860.9780.9940.0820.1681.02492.7
5.3-5.834.50.1297350.9850.9960.0680.1460.92399.1
5.83-6.674.50.1317410.9850.9960.0690.1490.88599.6
6.67-8.44.30.097530.9870.9970.0490.1030.81399.2
8.4-504.10.0667470.9860.9970.0370.0760.73396.5

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.08→48.01 Å / SU ML: 0.51 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 34.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3029 563 4.92 %Random selection
Rwork0.256 ---
obs0.2583 11439 76.76 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.08→48.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4633 0 14 0 4647
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044763
X-RAY DIFFRACTIONf_angle_d0.6866515
X-RAY DIFFRACTIONf_dihedral_angle_d18.373692
X-RAY DIFFRACTIONf_chiral_restr0.048738
X-RAY DIFFRACTIONf_plane_restr0.006843
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.08-3.390.3486860.33321667X-RAY DIFFRACTION47
3.39-3.880.3791160.30082428X-RAY DIFFRACTION69
3.88-4.880.31821790.2393286X-RAY DIFFRACTION93
4.88-48.010.26131820.24213495X-RAY DIFFRACTION97
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)
10.37110.18160.21691.4078-0.44212.14610.1148-0.12660.11180.4659-0.04330.28170.0922-1.0838-0.13610.8143-0.38360.43791.8881-0.18040.8554-7.9477.44856.38
22.403-0.7272-0.22470.97140.05830.9956-0.0996-0.84290.18230.35170.42420.3689-0.1013-1.16510.09010.52950.4031-0.04441.34460.05610.5731-1.0314.90358.702
31.4984-0.63290.47170.2761-0.25530.71750.0781-0.23990.57530.2349-0.09460.5911-0.7601-1.0942-0.10430.95210.53050.25120.9597-0.32220.93870.57925.75557.857
41.58250.009-0.38331.03680.18442.7609-0.04920.1367-0.1977-0.0436-0.23830.79670.0084-1.1277-0.14790.51830.06510.17120.860.04770.56860.4437.01447.226
50.3963-0.6208-0.78112.57140.26762.7071-0.26820.1772-0.3414-0.75420.30650.11420.079-1.8217-0.0310.8271-0.5529-0.13731.22360.1010.5811-7.7521.66336.907
60.8734-0.0883-0.70021.0968-0.66661.0621-0.03670.09130.1671-0.04930.16390.6680.4289-0.8037-0.00020.9265-0.65980.05931.07290.07011.5322-11.599-8.32323.843
72.167-0.67840.9372.52390.18233.73010.044-0.1066-0.41460.79690.21080.37930.207-1.16880.06630.5718-0.15430.18790.95490.21720.604-2.2075.57649.327
82.19490.3399-0.85161.3393-0.52583.61430.2827-0.09150.19540.3194-0.0619-0.2682-1.20350.0771-0.14970.6359-0.0222-0.02270.3536-0.10150.393721.83922.15531.274
90.9213-0.05482.16142.6668-0.85915.38750.1857-0.29880.18760.09730.1169-0.4252-0.75390.4922-0.16220.9193-0.2791-0.16940.4203-0.06580.231127.19524.70841.742
101.9919-0.4155-1.27862.88080.66314.38860.1064-0.1580.6752-0.42180.4137-0.4879-1.58850.2354-0.24650.918-0.1501-0.02030.4389-0.06820.472926.4627.84132.496
111.6562-0.26731.27592.01580.2062.1552-0.5468-0.33580.08060.26560.46480.0725-1.0650.1011-0.31230.6799-0.0352-0.02380.1752-0.040.419620.75519.29434.952
123.9756-0.2594-0.29211.9810.19195.11390.57890.29530.0675-0.0058-0.15630.4543-0.70810.11-0.04940.2999-0.03350.04070.55390.03550.453230.0913.956-2.796
131.591-0.6359-0.36961.86510.16783.84130.51110.11320.1958-0.1836-0.34360.0571-1.1408-0.0152-0.08530.57850.0320.0590.30680.01980.438630.29217.408-2.523
142.5271-0.8313-1.49181.8922-0.04162.142-0.1863-0.4892-0.58330.00670.3246-0.57090.67820.0702-0.33090.2882-0.2822-0.23130.31180.02090.667522.681-1.44235.836
152.5508-0.288-1.56291.236-0.50723.8016-0.08220.4636-0.426-0.0507-0.34820.30780.4177-1.1446-0.08390.726-0.11520.00330.4063-0.01420.39714.181.22533.263
162.9610.0786-0.30443.29581.28945.8396-0.31420.30480.5658-0.1065-0.12010.190.3092-0.0586-0.10940.53790.1587-0.12130.2812-0.1380.448121.6023.53132.56
171.46780.2451-1.27681.0588-0.81645.53410.0815-0.12340.1260.0428-0.13060.0010.23980.2578-0.00190.43230.0010.00950.2726-0.00840.469136.2293.693.62
183.2015-0.9332-2.15813.37411.92823.1-0.06380.35310.1110.0309-0.43940.2032-0.13860.5294-0.72360.6562-0.0771-0.15650.56540.14640.174837.4353.9867.669
191.1451-0.3006-0.6850.60390.47513.10830.0378-0.0030.10690.01450.1043-0.3656-0.43721.38640.1390.1046-0.2358-0.03110.46980.02540.498244.9273.308-1.562
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 334:353 )A334 - 353
2X-RAY DIFFRACTION2( CHAIN A AND RESID 354:380 )A354 - 380
3X-RAY DIFFRACTION3( CHAIN A AND RESID 381:393 )A381 - 393
4X-RAY DIFFRACTION4( CHAIN A AND RESID 394:447 )A394 - 447
5X-RAY DIFFRACTION5( CHAIN A AND RESID 448:477 )A448 - 477
6X-RAY DIFFRACTION6( CHAIN A AND RESID 478:487 )A478 - 487
7X-RAY DIFFRACTION7( CHAIN A AND RESID 488:528 )A488 - 528
8X-RAY DIFFRACTION8( CHAIN H AND RESID 1:52 )H1 - 52
9X-RAY DIFFRACTION9( CHAIN H AND RESID 53:67 )H53 - 67
10X-RAY DIFFRACTION10( CHAIN H AND RESID 68:87 )H68 - 87
11X-RAY DIFFRACTION11( CHAIN H AND RESID 88:119 )H88 - 119
12X-RAY DIFFRACTION12( CHAIN H AND RESID 120:165 )H120 - 165
13X-RAY DIFFRACTION13( CHAIN H AND RESID 166:214 )H166 - 214
14X-RAY DIFFRACTION14( CHAIN L AND RESID 3:38 )L3 - 38
15X-RAY DIFFRACTION15( CHAIN L AND RESID 39:75 )L39 - 75
16X-RAY DIFFRACTION16( CHAIN L AND RESID 76:101 )L76 - 101
17X-RAY DIFFRACTION17( CHAIN L AND RESID 102:150 )L102 - 150
18X-RAY DIFFRACTION18( CHAIN L AND RESID 151:174 )L151 - 174
19X-RAY DIFFRACTION19( CHAIN L AND RESID 175:209 )L175 - 209

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