[English] 日本語
Yorodumi
- PDB-9yxw: Crystal structure of HCoV-HKU1 RBD bound by H501-008 Fab -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9yxw
TitleCrystal structure of HCoV-HKU1 RBD bound by H501-008 Fab
Components
  • H501-008 Fab heavy chain
  • H501-008 Fab light chain
  • Spike protein S1
KeywordsVIRAL PROTEIN / HCoV-HKU1 / coronavirus / antibody / Fab
Function / homology
Function and homology information


host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated virion attachment to host cell / 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 / host cell plasma membrane / virion membrane / membrane / identical protein binding
Similarity search - Function
Spike (S) protein S1 subunit, receptor-binding domain, HKU1-like / Spike (S) protein S1 subunit, N-terminal domain, murine hepatitis virus-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. / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal ...Spike (S) protein S1 subunit, receptor-binding domain, HKU1-like / Spike (S) protein S1 subunit, N-terminal domain, murine hepatitis virus-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. / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / 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 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 speciesHuman coronavirus HKU1
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsWrapp, D. / McLellan, J.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01-AI127521 United States
CitationJournal: bioRxiv / Year: 2025
Title: Human Coronavirus HKU1 Neutralizing Monoclonal Antibodies Target Diverse Epitopes Within and Around the TMPRSS2 Receptor Binding Site.
Authors: Lingshu Wang / Jeswin Joseph / Sheena Vasquez / Daniel Wrapp / Timothy P Sheahan / Christian K O Dzuvor / Osnat Rosen / Robert N Kirchdoerfer / Olubukola M Abiona / Catherine Hammond / Wei ...Authors: Lingshu Wang / Jeswin Joseph / Sheena Vasquez / Daniel Wrapp / Timothy P Sheahan / Christian K O Dzuvor / Osnat Rosen / Robert N Kirchdoerfer / Olubukola M Abiona / Catherine Hammond / Wei Shi / Sydney P Moak / Wing-Pui Kong / Yi Zhang / Michael R Eso / Ariane J Brown / Andrew B Ward / Ralph Baric / Jason S McLellan / Theodore C Pierson / John Mascola / Barney S Graham / Hadi M Yassine / Christopher O Barnes / Kizzmekia S Corbett-Helaire /
Abstract: Endemic human coronaviruses (HCoVs), like HCoV-HKU1, account for ~30% of common cold/year and can cause serious upper and lower respiratory infections, yet no licensed vaccines target HCoVs. In fact, ...Endemic human coronaviruses (HCoVs), like HCoV-HKU1, account for ~30% of common cold/year and can cause serious upper and lower respiratory infections, yet no licensed vaccines target HCoVs. In fact, little is known about HCoV-HKU1's antigenic landscape. Thus, we characterized key interactions between HCoV-HKU1 spike (S) with monoclonal antibodies (mAbs) isolated from pre-pandemic HCoV-HKU1 convalescent PBMCs. We isolated 14 mAbs, which bound distinct S regions: receptor binding domain (RBD), N-terminal domain (NTD), and S2 subunit. Structural and functional studies revealed three groups of RBD-specific mAbs targeting diverse footprints within and around the TMPRSS2 receptor binding site, exemplified by: (1) The most potently neutralizing mAb, H501-022 (IC = 0.01 μg/mL), which recognizes the TMPRSS2 binding motif, thereby blocking receptor engagement; (2) mAb H501-008 (IC = 0.05 μg/mL) that binds a conserved, cross-reactive epitope outside of the TMPRSS2 binding site that is shared with HCoV-OC43; and (3) H501-018 (IC = 0.28 μg/mL) that recognizes both "up" and "down" RBD conformations at a distinct, non-overlapping site outside of the TMPRSS2 binding motif, distinguishing itself from H501-022 and H501-008, which bind exclusively to the "up" RBD conformation. These mAbs represent the first type-specific HCoV-HKU1 mAbs isolated from a convalescent donor. Our findings provide molecular insight into HCoV-HKU1 antibody recognition and neutralization mechanisms, importantly highlighting antigenic differences comparing HCoVs and pandemic CoVs - a critical step towards advancing universal CoV vaccine design.
History
DepositionOct 27, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2026Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Spike protein S1
H: H501-008 Fab heavy chain
L: H501-008 Fab light chain


Theoretical massNumber of molelcules
Total (without water)82,9333
Polymers82,9333
Non-polymers00
Water3,225179
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)104.460, 71.760, 174.480
Angle α, β, γ (deg.)90.00, 94.58, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Spike protein S1


Mass: 33949.086 Da / Num. of mol.: 1 / Fragment: receptor-binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human coronavirus HKU1 / Gene: S, 3 / Production host: Homo sapiens (human) / References: UniProt: Q0ZME7
#2: Antibody H501-008 Fab heavy chain


Mass: 26356.568 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: Antibody H501-008 Fab light chain


Mass: 22626.938 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 179 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.93 Å3/Da / Density % sol: 68.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Tris pH 8.5, 0.2 M MgCl2, 25% PEG 3350

-
Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.6→59.09 Å / Num. obs: 39783 / % possible obs: 99.8 % / Redundancy: 3.1 % / CC1/2: 0.919 / Net I/σ(I): 4.8
Reflection shellResolution: 2.6→2.71 Å / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2811 / CC1/2: 0.703

-
Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→57.97 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2667 1933 4.86 %
Rwork0.2515 --
obs0.2522 39782 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.6→57.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5480 0 0 179 5659
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095619
X-RAY DIFFRACTIONf_angle_d1.4417656
X-RAY DIFFRACTIONf_dihedral_angle_d13.371994
X-RAY DIFFRACTIONf_chiral_restr0.077846
X-RAY DIFFRACTIONf_plane_restr0.012994
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.660.31121340.32772676X-RAY DIFFRACTION99
2.67-2.740.33181460.31632689X-RAY DIFFRACTION100
2.74-2.820.32151320.30612640X-RAY DIFFRACTION99
2.82-2.910.38231480.30192721X-RAY DIFFRACTION100
2.91-3.010.30241220.29082713X-RAY DIFFRACTION100
3.01-3.130.31611360.28492659X-RAY DIFFRACTION100
3.13-3.280.26981470.26352682X-RAY DIFFRACTION100
3.28-3.450.27841380.26122690X-RAY DIFFRACTION100
3.45-3.660.24681360.24522702X-RAY DIFFRACTION100
3.66-3.950.24421570.262716X-RAY DIFFRACTION100
3.95-4.340.24581090.21352720X-RAY DIFFRACTION100
4.34-4.970.21391340.19482732X-RAY DIFFRACTION100
4.97-6.260.26061560.24282719X-RAY DIFFRACTION100
6.26-57.970.25461380.25242790X-RAY DIFFRACTION99
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)
11.8720.2646-0.81450.0506-0.11680.355-0.4459-0.9686-0.52480.10970.05870.0495-1.1061-0.43240.15233.0020.2903-0.92822.6721-0.02781.4491-16.2791-47.031971.7502
20.10580.0229-0.31751.07610.26011.22950.4953-1.6395-0.34110.7784-0.3635-0.35070.0621-0.376-0.21913.04090.4971-0.87983.658-0.11371.2597-15.3211-37.061869.7888
31.6874-1.12880.13572.1063-0.65541.06650.3223-0.1953-0.12051.0457-0.0574-0.82050.00870.69480.02692.33950.996-0.752.5521-0.31450.8413-22.7062-35.071347.3144
41.78590.6277-0.5750.2469-0.13990.5544-0.5849-0.35590.7473-0.47760.25410.1945-0.2560.28450.2871.47770.5538-0.0141.90040.06890.7489-32.7479-24.525230.6845
52.40231.1918-2.23083.8275-0.06552.405-0.61410.47390.18650.86171.1552-1.13250.08331.052-0.45231.58720.3141-0.0971.9769-0.18041.4503-25.5047-16.826435.4564
62.9392.7076-0.42553.38330.23530.47490.15630.48560.02220.70770.4144-0.12990.38270.0859-0.5221.72680.7624-0.25982.2779-0.17761.041-26.2694-28.847543.1811
70.24130.1938-0.19920.7953-0.08590.1379-0.2761-1.5254-0.49851.2806-0.3093-0.662-0.3242-0.76010.34162.65910.2611-0.85473.49340.14061.4095-15.1386-40.343966.1004
81.2021-1.4927-0.6422.01650.43941.5685-0.6232-1.4485-0.86381.32250.36060.85741.28240.636-0.20011.39720.50480.38711.10930.511.0141-51.2389-50.422626.9132
91.2571-1.11420.84682.50550.35332.5524-0.6993-1.6462-1.39881.45170.29560.64381.22410.6769-0.181.63930.72030.47571.55060.750.7929-50.9378-48.917230.2905
104.6588-0.40960.21764.8031.09675.7106-0.19520.0268-0.08580.11450.03490.2407-0.0952-0.19570.11870.1903-0.04180.06460.1664-0.01660.4097-75.4737-49.5613-3.1523
114.6385-0.6648-0.8033.438-0.17762.1663-0.2862-1.2736-0.08870.86040.27590.1460.17990.4276-0.03050.55750.13010.04220.65720.02330.5158-53.7155-29.479521.6167
123.70320.66-0.02512.03420.32220.9128-0.05380.0469-0.18440.137-0.00340.07660.0866-0.20720.0870.26890.01490.00030.22710.01340.3925-77.5332-37.96874.3012
134.83-4.7275-4.3544.87184.23554.1292-0.1039-0.5068-0.72310.83860.07121.24360.21850.23240.11430.5132-0.0080.04260.36960.10730.6366-81.445-38.028816.0924
142.27480.2183-0.48265.13770.22742.73040.0007-0.15880.10270.3274-0.09630.45880.0457-0.25980.12260.32440.0173-0.02620.2754-0.02110.4147-79.3856-36.64556.8423
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 326 through 371 )
2X-RAY DIFFRACTION2chain 'A' and (resid 372 through 437 )
3X-RAY DIFFRACTION3chain 'A' and (resid 438 through 478 )
4X-RAY DIFFRACTION4chain 'A' and (resid 479 through 507 )
5X-RAY DIFFRACTION5chain 'A' and (resid 508 through 528 )
6X-RAY DIFFRACTION6chain 'A' and (resid 529 through 568 )
7X-RAY DIFFRACTION7chain 'A' and (resid 569 through 606 )
8X-RAY DIFFRACTION8chain 'H' and (resid 2 through 56 )
9X-RAY DIFFRACTION9chain 'H' and (resid 57 through 111 )
10X-RAY DIFFRACTION10chain 'H' and (resid 112 through 214 )
11X-RAY DIFFRACTION11chain 'L' and (resid 2 through 107 )
12X-RAY DIFFRACTION12chain 'L' and (resid 108 through 151 )
13X-RAY DIFFRACTION13chain 'L' and (resid 152 through 162 )
14X-RAY DIFFRACTION14chain 'L' and (resid 163 through 210 )

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more