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- PDB-9ml8: Crystal structure of the SARS-CoV-2 RBD in complex with the rabbi... -

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Basic information

Entry
Database: PDB / ID: 9ml8
TitleCrystal structure of the SARS-CoV-2 RBD in complex with the rabbit M8b-B1 Fab
Components
  • M8b-B1 heavy chain
  • M8b-B1 light chain
  • Spike protein S1
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / immune system / neutralizing antibody / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


symbiont-mediated disruption of host tissue / Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / viral translation / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion ...symbiont-mediated disruption of host tissue / Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / viral translation / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / membrane fusion / entry receptor-mediated virion attachment to host cell / Attachment and Entry / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / host cell surface receptor binding / symbiont-mediated suppression of host innate immune response / receptor ligand activity / endocytosis involved in viral entry into host cell / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / symbiont entry into host cell / 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 / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, N-terminal domain superfamily / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Spike glycoprotein, betacoronavirus / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus ...Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, N-terminal domain superfamily / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Spike glycoprotein, betacoronavirus / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike (S) protein S1 subunit, receptor-binding domain, 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 superfamily, coronavirus / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2
Similarity search - Domain/homology
Biological speciesSevere acute respiratory syndrome coronavirus 2
Oryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsFan, C. / Bjorkman, P.J.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P01-AI165075 United States
Bill & Melinda Gates Foundation United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2025
Title: Cross-reactive sarbecovirus antibodies induced by mosaic RBD nanoparticles.
Authors: Chengcheng Fan / Jennifer R Keeffe / Kathryn E Malecek / Alexander A Cohen / Anthony P West / Viren A Baharani / Annie V Rorick / Han Gao / Priyanthi N P Gnanapragasam / Semi Rho / Jaasiel ...Authors: Chengcheng Fan / Jennifer R Keeffe / Kathryn E Malecek / Alexander A Cohen / Anthony P West / Viren A Baharani / Annie V Rorick / Han Gao / Priyanthi N P Gnanapragasam / Semi Rho / Jaasiel Alvarez / Luisa N Segovia / Theodora Hatziioannou / Paul D Bieniasz / Pamela J Bjorkman /
Abstract: Broad immune responses are needed to mitigate viral evolution and escape. To induce antibodies against conserved receptor-binding domain (RBD) regions of SARS-like betacoronavirus (sarbecovirus) ...Broad immune responses are needed to mitigate viral evolution and escape. To induce antibodies against conserved receptor-binding domain (RBD) regions of SARS-like betacoronavirus (sarbecovirus) spike proteins that recognize SARS-CoV-2 variants of concern and zoonotic sarbecoviruses, we developed mosaic-8b RBD nanoparticles presenting eight sarbecovirus RBDs arranged randomly on a 60-mer nanoparticle. Mosaic-8b immunizations protected animals from challenges from viruses whose RBDs were matched or mismatched to those on nanoparticles. Here, we describe neutralizing mAbs isolated from mosaic-8b-immunized rabbits, some on par with Pemgarda, the only currently FDA-approved therapeutic mAb. Deep mutational scanning, in vitro selection of spike resistance mutations, and single-particle cryo-electron microscopy structures of spike-antibody complexes demonstrated targeting of conserved RBD epitopes. Rabbit mAbs included critical D-gene segment RBD-recognizing features in common with human anti-RBD mAbs, despite rabbit genomes lacking an equivalent human D-gene segment, thus demonstrating that the immune systems of humans and other mammals can utilize different antibody gene segments to arrive at similar modes of antigen recognition. These results suggest that animal models can be used to elicit anti-RBD mAbs with similar properties to those raised in humans, which can then be humanized for therapeutic use, and that mosaic RBD nanoparticle immunization coupled with multiplexed screening represents an efficient way to generate and select broadly cross-reactive therapeutic pan-sarbecovirus and pan-SARS-CoV-2 variant mAbs.
History
DepositionDec 18, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 4, 2025Provider: 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
B: Spike protein S1
C: Spike protein S1
D: Spike protein S1
E: M8b-B1 heavy chain
F: M8b-B1 light chain
H: M8b-B1 heavy chain
L: M8b-B1 light chain
M: M8b-B1 heavy chain
N: M8b-B1 light chain
P: M8b-B1 heavy chain
Q: M8b-B1 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)291,68523
Polymers289,31512
Non-polymers2,37011
Water13,601755
1
A: Spike protein S1
H: M8b-B1 heavy chain
L: M8b-B1 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,9456
Polymers72,3293
Non-polymers6173
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Spike protein S1
E: M8b-B1 heavy chain
F: M8b-B1 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,8495
Polymers72,3293
Non-polymers5202
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Spike protein S1
M: M8b-B1 heavy chain
N: M8b-B1 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,9456
Polymers72,3293
Non-polymers6173
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Spike protein S1
P: M8b-B1 heavy chain
Q: M8b-B1 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,9456
Polymers72,3293
Non-polymers6173
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)175.074, 173.441, 129.928
Angle α, β, γ (deg.)90.000, 116.552, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

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Antibody , 2 types, 8 molecules EHMPFLNQ

#2: Antibody
M8b-B1 heavy chain


Mass: 24956.049 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Production host: Homo sapiens (human)
#3: Antibody
M8b-B1 light chain


Mass: 23367.736 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Production host: Homo sapiens (human)

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Protein / Sugars , 2 types, 8 molecules ABCD

#1: Protein
Spike protein S1


Mass: 24004.926 Da / Num. of mol.: 4 / Fragment: Receptor-Binding Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: S, 2 / Production host: Homo sapiens (human) / References: UniProt: P0DTC2
#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.: 4
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

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Non-polymers , 2 types, 762 molecules

#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 755 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 3.05 Å3/Da / Density % sol: 59.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M lithium sulfate 0.1 sodium citrate 20% (w/v) PEG 1,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jun 11, 2024
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.4→39.15 Å / Num. obs: 133293 / % possible obs: 98.5 % / Redundancy: 7.2 % / Biso Wilson estimate: 38.38 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.172 / Rpim(I) all: 0.068 / Rrim(I) all: 0.185 / Χ2: 0.92 / Net I/σ(I): 7.3
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.989 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 6593 / CC1/2: 0.769 / Rpim(I) all: 0.388 / Rrim(I) all: 1.063 / Χ2: 0.95 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→39.15 Å / SU ML: 0.3103 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.5508
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2468 1757 1.32 %
Rwork0.2227 131154 -
obs0.223 132911 98.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 55.2 Å2
Refinement stepCycle: LAST / Resolution: 2.4→39.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19488 0 147 755 20390
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002120215
X-RAY DIFFRACTIONf_angle_d0.530227562
X-RAY DIFFRACTIONf_chiral_restr0.04323053
X-RAY DIFFRACTIONf_plane_restr0.00373519
X-RAY DIFFRACTIONf_dihedral_angle_d14.24637218
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.460.35591370.283610170X-RAY DIFFRACTION98.92
2.46-2.540.31891350.275410060X-RAY DIFFRACTION98.94
2.54-2.620.30011340.265710109X-RAY DIFFRACTION98.92
2.62-2.710.33161360.274310087X-RAY DIFFRACTION98.82
2.71-2.820.2921360.260910109X-RAY DIFFRACTION98.6
2.82-2.950.27841280.24839675X-RAY DIFFRACTION94.58
2.95-3.110.31071370.252510173X-RAY DIFFRACTION99.4
3.11-3.30.26741360.244410184X-RAY DIFFRACTION99.55
3.3-3.550.24231360.233610177X-RAY DIFFRACTION99.4
3.55-3.910.23181370.210110178X-RAY DIFFRACTION99.22
3.91-4.480.21511320.18429854X-RAY DIFFRACTION95.84
4.48-5.640.19921370.178410250X-RAY DIFFRACTION99.74
5.64-39.150.19891360.210510128X-RAY DIFFRACTION97.39
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)
11.707517165640.920858419703-1.102602807681.75469321441-0.7447979666661.36490008299-0.00392816022032-0.0289804752548-0.0861605165658-0.0565931270632-0.0336493567644-0.0175962570471-0.1731843565440.03203412797260.01081712506990.325877262738-0.115995933818-0.06618557050450.4522990365790.05708755289090.25892159757140.548634826923.148598759915.5789387183
22.00126226538-1.360267362281.062720379762.05228447018-1.131034573911.497872187330.03015784672580.10683095792-0.1280851610040.08439191992470.0146732205618-0.104948199767-0.011855637784-0.0796612933621-0.04233493943560.4119681449540.116417075198-0.0868486138690.332522089524-0.06420086497990.286285834257-19.924211602814.421201724115.580846451
31.944936903521.38880240834-0.9844993506572.10821340894-1.626979615741.247376860320.148220928925-0.265423567430.2340488603180.0250644783845-0.0763020283448-0.0846457955514-0.034317626405-0.188694199939-0.04842850476660.480268760853-0.1549884176170.116697941620.397182984156-0.1045017906320.337283482629-20.070017704550.1604585461100.580545736
42.75914799775-2.106765491061.584432188152.01333084389-0.7181494483150.884564598503-0.148372667724-0.26392631640.1455734783030.3873020130220.2060560810290.153037578820.0406376970861-0.0993691367899-0.04424611618980.4626125271230.1745558742190.1100952741770.5846904733240.1354942617040.38575673202940.833074281140.8872165169100.580078234
50.4897995803750.124655507606-0.330106524363.100421206911.105396146581.596014421630.0009238418552-0.126515548597-0.02850224686610.663148434289-0.1800326690160.4858167222770.205425809238-0.08545917000610.01116435778390.3050779805920.00142121150110.09817907096690.267198984606-0.03980163138380.308347638399-3.263372497862.2360990207955.0349981642
60.1426193902770.0684033948662-0.656661185883.13423034991.796326971682.392291332080.04687538545950.01255086908650.1705872764120.705415264733-0.4505112338480.7524406551310.3169995168410.267305523283-0.07437515361680.435146027172-0.03921538316170.1411007601210.318681208088-0.1229928371250.404095394449-8.5257182322118.54286885863.0863827646
72.80073199390.002750343101151.044653237190.7467648031570.7074714975571.29592876755-0.179321005089-0.6244999361860.3927381575860.205559534743-0.0637527540326-0.0379161801972-0.000580285320607-0.219232013347-0.004856888175470.2585939465420.00342677337167-0.05228355792630.344801963925-0.07816509771540.32433608398228.28154188316.6512945729755.0703725884
82.67965012063-0.05899402295711.418963978730.1211557812970.6691163687222.33142193297-0.34349257412-0.5742461305860.5471374257220.0310323994680.125625385594-0.07110530887530.246296046567-0.2869754684350.03569283111670.3633060375780.0364043765448-0.1178571391340.44040548652-0.09229573277860.39711863880644.736603448911.732401801563.0529652928
90.849354604954-0.02230999205190.3344738941213.144432690781.357501799761.68450507948-0.05479435118330.156441024077-0.00365132202504-0.727490230056-0.1702742238740.446153896674-0.31225487966-0.04710243378870.0002253430247980.342481562119-0.0155023510111-0.1147249570210.230660010885-0.04829551610990.357941377339-3.2009459797662.098550917661.2368057229
100.003964499227080.1817621693670.4454827051552.820844919781.646876991651.359218143620.08220958610830.0532563529142-0.154532500679-0.65706501638-0.3096988323690.669533009837-0.403379106329-0.0741590328730.1441104807620.4529734675750.05925673994-0.1156718474730.338823210777-0.1294662984770.439502986025-8.5025488074745.838214304953.24174312
112.91792483795-0.213281474816-1.285983000760.8518500545620.5685560046471.27935139377-0.1767034349490.591874073958-0.524050548593-0.154682479895-0.06695973380730.01572873685270.0905604034598-0.3006356309050.08243456176130.231733753243-0.01094262582360.02849623234220.307751953219-0.1198018456850.36919830390328.309847260657.621240591561.2051781369
122.736761255320.0594649008918-1.27065433361-0.01263167152130.664922315832.30917177944-0.3697180495720.558993723456-0.7436364757310.01223647733180.0862454148333-0.100275068605-0.330420120611-0.3333515373060.0871974211510.361881376846-0.03067055887960.1106083337860.434841660568-0.1231654445850.49192967176244.823099053252.517161544853.3697052335
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain 'A' and resid 333 through 528)AA333 - 5281 - 196
22(chain 'B' and resid 333 through 528)BD333 - 5281 - 196
33(chain 'C' and resid 333 through 528)CG333 - 5281 - 196
44(chain 'D' and resid 333 through 528)DJ333 - 5281 - 196
55(chain 'E' and resid 2 through 214)EM2 - 2141 - 224
66(chain 'F' and resid 1 through 213)FN1 - 2131 - 216
77(chain 'H' and resid 2 through 214)HO2 - 2141 - 224
88(chain 'L' and resid 1 through 213)LP1 - 2131 - 216
99(chain 'M' and resid 2 through 214)MQ2 - 2141 - 224
1010(chain 'N' and resid 1 through 213)NR1 - 2131 - 216
1111(chain 'P' and resid 2 through 214)PS2 - 2141 - 224
1212(chain 'Q' and resid 1 through 212)QT1 - 2121 - 215

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