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- PDB-7ean: immune complex of SARS-CoV-2 RBD and cross-neutralizing antibody 6D6 -

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Basic information

Entry
Database: PDB / ID: 7ean
Titleimmune complex of SARS-CoV-2 RBD and cross-neutralizing antibody 6D6
Components
  • Heavy chain of SARS-CoV-2 cross-neutralizing mAb 6D6
  • Light chain of SARS-CoV-2 cross-neutralizing mAb 6D6
  • Spike protein S1
KeywordsVIRAL PROTEIN / SARS-CoV-2 / Receptor binding domain / neutralizing antibody / immune complex
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 / host cell endoplasmic reticulum-Golgi intermediate compartment membrane ...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 / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / entry receptor-mediated virion attachment to host cell / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / membrane fusion / 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 / membrane / identical protein binding / 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
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 Å
AuthorsLi, T.T. / Gu, Y. / Li, S.W.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82001756 China
CitationJournal: Nat Commun / Year: 2021
Title: Cross-neutralizing antibodies bind a SARS-CoV-2 cryptic site and resist circulating variants.
Authors: Li, T. / Xue, W. / Zheng, Q. / Song, S. / Yang, C. / Xiong, H. / Zhang, S. / Hong, M. / Zhang, Y. / Yu, H. / Zhang, Y. / Sun, H. / Huang, Y. / Deng, T. / Chi, X. / Li, J. / Wang, S. / Zhou, ...Authors: Li, T. / Xue, W. / Zheng, Q. / Song, S. / Yang, C. / Xiong, H. / Zhang, S. / Hong, M. / Zhang, Y. / Yu, H. / Zhang, Y. / Sun, H. / Huang, Y. / Deng, T. / Chi, X. / Li, J. / Wang, S. / Zhou, L. / Chen, T. / Wang, Y. / Cheng, T. / Zhang, T. / Yuan, Q. / Zhao, Q. / Zhang, J. / McLellan, J.S. / Zhou, Z.H. / Zhang, Z. / Li, S. / Gu, Y. / Xia, N.
History
DepositionMar 7, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 31, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 6, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 29, 2023Group: 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

Downloads & links

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Assembly

Deposited unit
A: Spike protein S1
H: Heavy chain of SARS-CoV-2 cross-neutralizing mAb 6D6
L: Light chain of SARS-CoV-2 cross-neutralizing mAb 6D6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,4134
Polymers72,1913
Non-polymers2211
Water2,972165
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5770 Å2
ΔGint-24 kcal/mol
Surface area27610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.280, 85.340, 160.710
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Spike protein S1


Mass: 25122.336 Da / Num. of mol.: 1
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 Heavy chain of SARS-CoV-2 cross-neutralizing mAb 6D6


Mass: 23743.328 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#3: Antibody Light chain of SARS-CoV-2 cross-neutralizing mAb 6D6


Mass: 23325.701 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) 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 / Feature type: SUBJECT OF INVESTIGATION
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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 293.15 K / Method: evaporation / Details: 0.2M sodium sulfocyanate, 20%PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 2, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.91→30.08 Å / Num. obs: 119757 / % possible obs: 99.8 % / Redundancy: 6.7 % / Biso Wilson estimate: 42.88 Å2 / CC1/2: 0.999 / Rpim(I) all: 2.7 / Rsym value: 0.064 / Net I/σ(I): 13.7
Reflection shellResolution: 1.91→1.96 Å / Num. unique obs: 6201 / CC1/2: 0.402 / Rpim(I) all: 0.913

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6M0J, 1WEJ

6m0j

1wej


Resolution: 1.91→29.251 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2239 3809 3.18 %
Rwork0.1911 115948 -
obs0.1921 119757 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 220.1 Å2 / Biso mean: 64.0735 Å2 / Biso min: 30.68 Å2
Refinement stepCycle: final / Resolution: 1.91→29.251 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4853 0 28 165 5046
Biso mean--125.67 53.5 -
Num. residues----627
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.91-1.93420.41491360.3998427699
1.9342-1.95960.32931430.35564281100
1.9596-1.98650.36491430.32734370100
1.9865-2.01480.35231400.30784244100
2.0148-2.04490.29561390.34285100
2.0449-2.07690.37331350.3644425398
2.0769-2.11090.32061430.28424288100
2.1109-2.14730.23941450.26734322100
2.1473-2.18630.35391380.26074275100
2.1863-2.22840.27021440.2524303100
2.2284-2.27380.3511450.2771423799
2.2738-2.32320.3281420.23024338100
2.3232-2.37730.261430.21884298100
2.3773-2.43670.27951400.21054304100
2.4367-2.50250.20881450.20474278100
2.5025-2.57610.2431360.19654329100
2.5761-2.65920.191430.19424312100
2.6592-2.75420.20391420.19274281100
2.7542-2.86440.21631390.19354304100
2.8644-2.99460.27841440.19764279100
2.9946-3.15230.231400.18874339100
3.1523-3.34960.23471430.18884321100
3.3496-3.60780.2021420.17454309100
3.6078-3.970.171410.1654286100
3.97-4.54270.17761430.1414286100
4.5427-5.71630.19941380.1484320100
5.7163-29.2510.21671370.1943423098
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)
12.2290.7126-0.17833.48970.63133.1186-0.37121.18070.05390.07590.1566-0.3497-0.2770.53690.2960.5074-0.0367-0.0270.5461-0.05990.590334.553734.292131.4496
29.11390.65041.27741.0871-0.50160.942-0.27710.41430.0024-0.0820.2036-0.3229-0.13410.37010.13120.41610.0114-0.01250.6471-0.13990.460132.870525.871930.6864
31.50030.71671.11693.88011.58583.1488-0.1614-0.60940.13040.58430.2847-0.6244-0.02260.3624-0.13450.5870.0496-0.08620.7461-0.10860.568337.324627.336344.9741
46.2475-1.89292.27575.927-0.3592.254-0.1174-0.61350.27970.38850.14340.1744-0.114-0.3920.02770.47170.0137-0.03710.6222-0.10830.397923.042327.647938.5235
54.38435.20121.44836.6591.31832.07840.5555-0.9522-0.3030.8311-0.3590.4990.7809-0.5272-0.04440.5340.00270.07320.79030.00660.459716.12821.108340.9414
65.44880.63921.89243.71231.52583.3038-0.2078-0.60390.47290.2512-0.01280.2127-0.3091-0.36860.20490.38650.06840.01160.5888-0.05710.347918.754329.930136.1166
78.16121.2534-0.19543.46130.88661.79750.0012-0.0717-0.1237-0.0489-0.07670.55020.093-0.79930.07510.4204-0.01120.010.70780.01980.40736.018721.488727.3502
84.21470.41420.18363.18831.1522.4978-0.3813-0.93170.46480.44650.3817-0.14270.01080.0960.05060.44850.0565-0.07290.5468-0.06420.344727.469829.307738.3931
91.8940.532-0.25831.3370.85144.2074-0.00680.0820.033-0.0937-0.02740.0055-0.1-0.20060.03260.38290.00730.01010.38120.01390.396922.529718.61456.9763
109.6451-5.4462-5.22978.36255.24377.2872-0.0286-0.17850.29540.2357-0.1239-0.1484-0.38170.2285-0.16670.4824-0.01550.00830.43390.02620.460332.42325.542110.1469
113.29932.14381.77743.6874-0.89314.7969-0.03670.21140.5324-0.05180.0725-0.0645-0.3135-0.1995-0.07640.49220.02650.0090.37860.02130.443524.355426.74995.0561
125.26130.0292-3.57663.3429-0.41712.7604-0.12410.0987-0.1733-0.25660.1193-0.38720.1110.17390.00770.3880.0157-0.00560.41540.00320.410727.635715.48970.2477
131.43490.64370.89341.40050.47032.09080.04780.0897-0.1065-0.12460.1139-0.05110.07080.1724-0.06320.35410.00470.00710.41570.01790.400118.921613.02213.8612
145.98962.7809-3.24144.2359-1.13764.4275-0.10030.0229-0.3383-0.00560.02250.2790.6314-0.35480.02190.5024-0.0328-0.05030.38020.04280.45515.8337-2.6264-3.1302
157.0515.1626-0.65356.6622-1.01530.69460.0866-0.1669-0.0708-0.17620.03020.85460.245-0.1887-0.10860.5282-0.0239-0.07620.48180.07540.7376-2.26162.496-4.8636
163.12140.07060.42571.03451.03092.7139-0.0827-0.2017-0.2184-0.20030.1475-0.25040.68650.3024-0.13250.51840.1051-0.06030.46960.05840.573629.6929-3.786317.9996
171.57350.2874-0.6032.9970.47592.16840.1129-0.3181-0.23540.0809-0.018-0.00010.25390.1231-0.10410.45150.0284-0.04160.5140.06610.450126.78335.220423.2565
183.13872.9723-1.63484.5224-1.49172.67110.05520.0044-0.57750.17120.14-0.22720.3758-0.0246-0.14560.4650.0429-0.05180.45290.05340.499721.6074-0.285718.8767
191.76340.88670.94541.40110.79051.4990.03940.0385-0.3035-0.21760.0767-0.00270.34110.0202-0.11050.62970.0285-0.01580.39120.00870.510214.4355-6.78012.4404
208.2122.38824.78525.18554.41634.8217-0.20220.38-1.1859-0.61120.64210.06111.46420.13-0.35251.0827-0.0246-0.12260.5457-0.17220.818411.048-21.2702-13.2506
212.00470.94581.53871.308-1.16456.96520.03420.052-0.1795-0.0144-0.1436-0.1534-0.24220.224-0.02880.66270.0202-0.09860.36420.00710.655614.32-10.19571.6924
225.37730.04571.53953.1224-0.19226.1955-0.0410.6906-0.202-1.05220.2976-0.01480.47980.2788-0.05971.1219-0.1214-0.11360.5058-0.07830.62267.507-11.8792-18.4327
230.817-1.4041.66283.0299-4.60587.6564-0.03370.3417-0.4876-0.48180.15490.00860.6956-0.21740.00281.0154-0.081-0.16890.4848-0.09670.78165.6685-21.8371-7.4876
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 333 through 349 )A333 - 349
2X-RAY DIFFRACTION2chain 'A' and (resid 350 through 364 )A350 - 364
3X-RAY DIFFRACTION3chain 'A' and (resid 365 through 393 )A365 - 393
4X-RAY DIFFRACTION4chain 'A' and (resid 394 through 409 )A394 - 409
5X-RAY DIFFRACTION5chain 'A' and (resid 410 through 421 )A410 - 421
6X-RAY DIFFRACTION6chain 'A' and (resid 422 through 459 )A422 - 459
7X-RAY DIFFRACTION7chain 'A' and (resid 460 through 494 )A460 - 494
8X-RAY DIFFRACTION8chain 'A' and (resid 495 through 527 )A495 - 527
9X-RAY DIFFRACTION9chain 'H' and (resid 1 through 52 )H1 - 52
10X-RAY DIFFRACTION10chain 'H' and (resid 53 through 64 )H53 - 64
11X-RAY DIFFRACTION11chain 'H' and (resid 65 through 83 )H65 - 83
12X-RAY DIFFRACTION12chain 'H' and (resid 84 through 98 )H84 - 98
13X-RAY DIFFRACTION13chain 'H' and (resid 99 through 132 )H99 - 132
14X-RAY DIFFRACTION14chain 'H' and (resid 133 through 192 )H133 - 192
15X-RAY DIFFRACTION15chain 'H' and (resid 193 through 222 )H193 - 222
16X-RAY DIFFRACTION16chain 'L' and (resid 1 through 18 )L1 - 18
17X-RAY DIFFRACTION17chain 'L' and (resid 19 through 75 )L19 - 75
18X-RAY DIFFRACTION18chain 'L' and (resid 76 through 90 )L76 - 90
19X-RAY DIFFRACTION19chain 'L' and (resid 91 through 143 )L91 - 143
20X-RAY DIFFRACTION20chain 'L' and (resid 144 through 154 )L144 - 154
21X-RAY DIFFRACTION21chain 'L' and (resid 155 through 173 )L155 - 173
22X-RAY DIFFRACTION22chain 'L' and (resid 174 through 187 )L174 - 187
23X-RAY DIFFRACTION23chain 'L' and (resid 188 through 210 )L188 - 210

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