[English] 日本語
Yorodumi
- PDB-9ehu: Crystal structure of the Gamak virus attachment protein head domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9ehu
TitleCrystal structure of the Gamak virus attachment protein head domain
ComponentsGamak virus attachment protein head domain
KeywordsVIRAL PROTEIN / fusion / glycoprotein / virus
Biological speciesMeasles morbillivirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 Å
AuthorsLindenberger, J. / Acharya, P.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI165147 United States
CitationJournal: bioRxiv / Year: 2025
Title: Structural and Antigenic Characterization of Novel and Diverse Glycoproteins.
Authors: Aaron J May / Muralikrishna Lella / Jared Lindenberger / Alex Berkman / Ujjwal Kumar / Moumita Dutta / Maggie Barr / Rob Parks / Amanda Newman / Xiao Huang / Kijun Song / Victor Ilevbare / ...Authors: Aaron J May / Muralikrishna Lella / Jared Lindenberger / Alex Berkman / Ujjwal Kumar / Moumita Dutta / Maggie Barr / Rob Parks / Amanda Newman / Xiao Huang / Kijun Song / Victor Ilevbare / Salam Sammour / Chan Soo Park / Radha Devkota Adhikari / Priyanka Devkota / Katarzyna Janowska / Yanshun Liu / Garrett Scapellato / Taylor N Spence / Katayoun Mansouri / Robert J Edwards / Kevin O Saunders / Barton F Haynes / Priyamvada Acharya /
Abstract: Henipaviruses, a genus within the family, include the highly virulent Nipah and Hendra viruses that cause reoccurring outbreaks of deadly disease . Recent discoveries of several new species, ...Henipaviruses, a genus within the family, include the highly virulent Nipah and Hendra viruses that cause reoccurring outbreaks of deadly disease . Recent discoveries of several new species, including the zoonotic Langya virus , have revealed much higher antigenic diversity than currently characterized and prompted the reorganization of these viruses into the and genera . Here, to explore the limits of structural and antigenic variation in both genera, collectively referred to here as HNVs, we constructed an expanded, antigenically diverse panel of HNV fusion and attachment glycoproteins from 56 unique HNV strains that better reflects global HNV diversity. We expressed and purified the fusion protein ectodomains and the attachment protein head domains and characterized their biochemical, biophysical and structural properties. We performed immunization experiments in mice leading to the elicitation of antibodies reactive to multiple HNV fusion proteins. Cryo-electron microscopy structures of diverse fusion proteins elucidated molecular determinants of differential pre-fusion state metastability and higher order contacts. A crystal structure of the Gamak virus attachment head domain revealed an additional domain added to the conserved 6-bladed, β-propeller fold. Taken together, these studies expand the known structural and antigenic limits of the HNVs, reveal new cross-reactive epitopes within both genera and provide foundational data for the development of broadly reactive countermeasures.
History
DepositionNov 25, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 12, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Gamak virus attachment protein head domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,7069
Polymers52,5631
Non-polymers1,1428
Water4,035224
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)85.479, 85.479, 162.621
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Gamak virus attachment protein head domain


Mass: 52563.352 Da / Num. of mol.: 1 / Fragment: Head domain with 8x histidine tag
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Measles morbillivirus / Production host: Homo sapiens (human)

-
Sugars , 2 types, 2 molecules

#2: 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.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam 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
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: 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: isolated from a genetically manipulated source
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

-
Non-polymers , 4 types, 230 molecules

#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 224 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.26 Å3/Da / Density % sol: 62.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.1
Details: 0.2 M magnesium sulfate heptahydrate, 20% w/v PEG3350 at pH 7.1

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Oct 24, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.42→67.38 Å / Num. obs: 127371 / % possible obs: 97.09 % / Redundancy: 16.8 % / Biso Wilson estimate: 21.83 Å2 / Rmerge(I) obs: 0.17 / Net I/σ(I): 10.4
Reflection shellResolution: 1.42→1.43 Å / Rmerge(I) obs: 7.497 / Num. unique obs: 5851 / Rpim(I) all: 2.381

-
Processing

Software
NameVersionClassification
PHENIX1.21rc1_5127refinement
PHASERphasing
MOSFLMdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.42→67.38 Å / SU ML: 0.222 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.5157
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2265 6509 5.13 %
Rwork0.2094 120360 -
obs0.2102 126869 97.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.73 Å2
Refinement stepCycle: LAST / Resolution: 1.42→67.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3462 0 70 224 3756
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00563609
X-RAY DIFFRACTIONf_angle_d0.85824929
X-RAY DIFFRACTIONf_chiral_restr0.0837577
X-RAY DIFFRACTIONf_plane_restr0.0062619
X-RAY DIFFRACTIONf_dihedral_angle_d15.16191253
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.42-1.430.42641540.42383645X-RAY DIFFRACTION87.9
1.43-1.450.41782160.41353677X-RAY DIFFRACTION89.82
1.45-1.470.39411870.38173799X-RAY DIFFRACTION92.46
1.47-1.490.40091780.36483777X-RAY DIFFRACTION92.64
1.49-1.510.32631940.35463836X-RAY DIFFRACTION92.75
1.51-1.530.33961920.32943810X-RAY DIFFRACTION92.98
1.53-1.550.33262360.31383813X-RAY DIFFRACTION94.65
1.55-1.570.28412120.28973909X-RAY DIFFRACTION94.89
1.57-1.60.32062330.28423838X-RAY DIFFRACTION94.96
1.6-1.620.30282340.28143879X-RAY DIFFRACTION95.5
1.62-1.650.3032110.28093975X-RAY DIFFRACTION96.16
1.65-1.680.28252290.26573952X-RAY DIFFRACTION96.78
1.68-1.710.26782110.27064009X-RAY DIFFRACTION97.66
1.71-1.750.31032220.27264007X-RAY DIFFRACTION98.19
1.75-1.790.28142150.25814094X-RAY DIFFRACTION98.63
1.79-1.830.26042090.23854052X-RAY DIFFRACTION98.95
1.83-1.870.23972390.22624080X-RAY DIFFRACTION99.42
1.87-1.920.24992450.20814039X-RAY DIFFRACTION99.54
1.92-1.980.20271960.19164182X-RAY DIFFRACTION99.66
1.98-2.050.22192210.1884090X-RAY DIFFRACTION99.95
2.05-2.120.20912520.19454090X-RAY DIFFRACTION100
2.12-2.20.21052510.19754126X-RAY DIFFRACTION99.98
2.2-2.30.21092260.19214141X-RAY DIFFRACTION100
2.3-2.420.22071990.18614184X-RAY DIFFRACTION100
2.42-2.580.19942190.19664134X-RAY DIFFRACTION99.98
2.58-2.780.22922350.19694158X-RAY DIFFRACTION99.98
2.78-3.050.21072380.18974214X-RAY DIFFRACTION100
3.06-3.50.19512090.18564190X-RAY DIFFRACTION99.93
3.5-4.410.21732110.18434255X-RAY DIFFRACTION99.4
4.41-67.380.19282350.20154405X-RAY DIFFRACTION99.12

+
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