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- PDB-7k8p: Crystal structure of an anti-SARS-CoV-2 human neutralizing antibo... -

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Database: PDB / ID: 7k8p
TitleCrystal structure of an anti-SARS-CoV-2 human neutralizing antibody Fab fragment, C110
  • C110 Fab Heavy Chain
  • C110 Fab Light Chain
KeywordsIMMUNE SYSTEM / Human Neutralizing Antibody / SARS-CoV-2 / Receptor Binding Domain / COVID-19
Biological speciesHomo sapiens (human)
AuthorsDam, K.A. / Barnes, C.O. / Bjorkman, P.J.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P01-AI138938-S1 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P50 AI150464-13 United States
CitationJournal: Nature / Year: 2020
Title: SARS-CoV-2 neutralizing antibody structures inform therapeutic strategies.
Authors: Christopher O Barnes / Claudia A Jette / Morgan E Abernathy / Kim-Marie A Dam / Shannon R Esswein / Harry B Gristick / Andrey G Malyutin / Naima G Sharaf / Kathryn E Huey-Tubman / Yu E Lee / ...Authors: Christopher O Barnes / Claudia A Jette / Morgan E Abernathy / Kim-Marie A Dam / Shannon R Esswein / Harry B Gristick / Andrey G Malyutin / Naima G Sharaf / Kathryn E Huey-Tubman / Yu E Lee / Davide F Robbiani / Michel C Nussenzweig / Anthony P West / Pamela J Bjorkman /
Abstract: The coronavirus disease 2019 (COVID-19) pandemic presents an urgent health crisis. Human neutralizing antibodies that target the host ACE2 receptor-binding domain (RBD) of the severe acute ...The coronavirus disease 2019 (COVID-19) pandemic presents an urgent health crisis. Human neutralizing antibodies that target the host ACE2 receptor-binding domain (RBD) of the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) spike protein show promise therapeutically and are being evaluated clinically. Here, to identify the structural correlates of SARS-CoV-2 neutralization, we solved eight new structures of distinct COVID-19 human neutralizing antibodies in complex with the SARS-CoV-2 spike trimer or RBD. Structural comparisons allowed us to classify the antibodies into categories: (1) neutralizing antibodies encoded by the VH3-53 gene segment with short CDRH3 loops that block ACE2 and bind only to 'up' RBDs; (2) ACE2-blocking neutralizing antibodies that bind both up and 'down' RBDs and can contact adjacent RBDs; (3) neutralizing antibodies that bind outside the ACE2 site and recognize both up and down RBDs; and (4) previously described antibodies that do not block ACE2 and bind only to up RBDs. Class 2 contained four neutralizing antibodies with epitopes that bridged RBDs, including a VH3-53 antibody that used a long CDRH3 with a hydrophobic tip to bridge between adjacent down RBDs, thereby locking the spike into a closed conformation. Epitope and paratope mapping revealed few interactions with host-derived N-glycans and minor contributions of antibody somatic hypermutations to epitope contacts. Affinity measurements and mapping of naturally occurring and in vitro-selected spike mutants in 3D provided insight into the potential for SARS-CoV-2 to escape from antibodies elicited during infection or delivered therapeutically. These classifications and structural analyses provide rules for assigning current and future human RBD-targeting antibodies into classes, evaluating avidity effects and suggesting combinations for clinical use, and provide insight into immune responses against SARS-CoV-2.
DepositionSep 27, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 21, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 13, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

Structure visualization

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Deposited unit
H: C110 Fab Heavy Chain
L: C110 Fab Light Chain

Theoretical massNumber of molelcules
Total (without water)49,5192

  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3170 Å2
ΔGint-23 kcal/mol
Surface area18820 Å2
Unit cell
Length a, b, c (Å)48.498, 62.738, 78.423
Angle α, β, γ (deg.)90.000, 97.508, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z


#1: Antibody C110 Fab Heavy Chain

Mass: 25866.020 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#2: Antibody C110 Fab Light Chain

Mass: 23653.180 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#3: Water ChemComp-HOH / water / Water

Mass: 18.015 Da / Num. of mol.: 170 / Source method: isolated from a natural source / Formula: H2O

Experimental details


ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

Sample preparation

CrystalDensity Matthews: 2.39 Å3/Da / Density % sol: 48.51 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.3
Details: 0.2 M sodium tartrate dibasic dihydrate, 20 % w/v PEG3350

Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 19, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.8→38.9 Å / Num. obs: 42891 / % possible obs: 98.8 % / Redundancy: 4.7 % / Biso Wilson estimate: 23.83 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.041 / Net I/σ(I): 7.7
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 2 % / Rmerge(I) obs: 1.07 / Mean I/σ(I) obs: 2 / Num. unique obs: 4284 / CC1/2: 0.78 / Rpim(I) all: 0.82 / % possible all: 78.2


Blu-Icedata collection
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6XCA
Resolution: 1.8→38.69 Å / SU ML: 0.2005 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.6076
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2292 2181 5.09 %
Rwork0.1964 40681 -
obs0.1981 42862 98.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.97 Å2
Refinement stepCycle: LAST / Resolution: 1.8→38.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3171 0 0 170 3341
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01043255
X-RAY DIFFRACTIONf_angle_d1.20954448
X-RAY DIFFRACTIONf_chiral_restr0.0936504
X-RAY DIFFRACTIONf_plane_restr0.0081568
X-RAY DIFFRACTIONf_dihedral_angle_d13.5286455
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.840.30681470.27792513X-RAY DIFFRACTION98.92
1.84-1.880.32671390.25172540X-RAY DIFFRACTION99.52
1.88-1.930.26861340.22332543X-RAY DIFFRACTION99.33
1.93-1.980.26181260.21462553X-RAY DIFFRACTION99.15
1.98-2.040.24611320.21072507X-RAY DIFFRACTION98.65
2.04-2.110.21261340.19342529X-RAY DIFFRACTION98.08
2.11-2.180.2381290.19882500X-RAY DIFFRACTION97.51
2.18-2.270.23341410.19722546X-RAY DIFFRACTION99.52
2.27-2.370.26491360.21972533X-RAY DIFFRACTION99.22
2.37-2.50.25011250.21372562X-RAY DIFFRACTION99.3
2.5-2.650.24481460.21582552X-RAY DIFFRACTION99.41
2.65-2.860.22841430.21962559X-RAY DIFFRACTION99.12
2.86-3.140.26911330.21052483X-RAY DIFFRACTION96.42
3.14-3.60.25281470.19842575X-RAY DIFFRACTION99.93
3.6-4.530.1771270.16362591X-RAY DIFFRACTION99.56
4.53-38.690.18571420.16762595X-RAY DIFFRACTION97.65
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
Refinement TLS group


IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'H' and (resid 1 through 17 )HA1 - 171 - 17
22chain 'H' and (resid 18 through 40 )HA18 - 4018 - 40
33chain 'H' and (resid 41 through 91 )HA41 - 9141 - 95
44chain 'H' and (resid 92 through 114 )HA92 - 11496 - 129
55chain 'H' and (resid 115 through 212 )HA115 - 212130 - 216
66chain 'L' and (resid 2 through 18 )LB2 - 181 - 17
77chain 'L' and (resid 19 through 61 )LB19 - 6118 - 60
88chain 'L' and (resid 62 through 75 )LB62 - 7561 - 74
99chain 'L' and (resid 76 through 90 )LB76 - 9075 - 89
1010chain 'L' and (resid 91 through 113 )LB91 - 11390 - 112
1111chain 'L' and (resid 114 through 163 )LB114 - 163113 - 162
1212chain 'L' and (resid 164 through 211 )LB164 - 211163 - 212

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