[English] 日本語
Yorodumi
- PDB-9mer: Structure of H1H5:FluA20 Chimeric Influenza HA Complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9mer
TitleStructure of H1H5:FluA20 Chimeric Influenza HA Complex
Components
  • FluA20 Heavy Chain Fab
  • FluA20 Light Chain Fab
  • H1H5 HA
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / Influenza / Hemagglutinins / HA / Chimera H1 / H5 / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology: / DI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciesInfluenza A virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSeraj, N.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private United States
CitationJournal: Biorxiv / Year: 2025
Title: Structure-based Design of Chimeric Influenza Hemagglutinins to Elicit Cross-group Immunity.
Authors: Castro, K.M. / Ayardulabi, R. / Wehrle, S. / Cui, H. / Georgeon, S. / Schmidt, J. / Xiao, S. / Seraj, N. / Harshbarger, W. / Mallett, C.P. / Vassilev, V. / Saelens, X. / Correia, B.E.
History
DepositionDec 8, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 19, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: H1H5 HA
H: FluA20 Heavy Chain Fab
L: FluA20 Light Chain Fab
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,47837
Polymers74,2373
Non-polymers2,24134
Water8,593477
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)79.533, 79.533, 256.452
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

-
Components

-
Antibody , 2 types, 2 molecules HL

#2: Antibody FluA20 Heavy Chain Fab


Mass: 25154.039 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 FluA20 Light Chain Fab


Mass: 23508.186 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

-
Protein / Sugars , 2 types, 2 molecules B

#1: Protein H1H5 HA


Mass: 25574.566 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Production host: Homo sapiens (human)
#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

-
Non-polymers , 4 types, 510 molecules

#5: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 477 / 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: 2.73 Å3/Da / Density % sol: 54.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 0.2 M ammonium nitrate, 20% w/v PEG3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 2, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→46.98 Å / Num. obs: 92614 / % possible obs: 97.16 % / Redundancy: 3 % / Biso Wilson estimate: 23.83 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.031 / Net I/σ(I): 21.6
Reflection shellResolution: 2→2.072 Å / Num. unique obs: 4365 / CC1/2: 0.791 / % possible all: 78.83

-
Processing

Software
NameVersionClassification
PHENIX1-21.2-5419refinement
PHENIXmodel building
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→46.98 Å / SU ML: 0.2179 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.6818
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2151 3357 3.62 %
Rwork0.2059 89257 -
obs0.2062 92614 86.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.63 Å2
Refinement stepCycle: LAST / Resolution: 2→46.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5050 0 134 477 5661
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01425339
X-RAY DIFFRACTIONf_angle_d1.65727229
X-RAY DIFFRACTIONf_chiral_restr0.093797
X-RAY DIFFRACTIONf_plane_restr0.0092922
X-RAY DIFFRACTIONf_dihedral_angle_d15.72351962
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.030.2844590.28641624X-RAY DIFFRACTION38.14
2.03-2.060.3127740.271979X-RAY DIFFRACTION46.38
2.06-2.090.3309870.26032264X-RAY DIFFRACTION52.12
2.09-2.120.2384960.23732574X-RAY DIFFRACTION60.2
2.12-2.160.27881100.24842758X-RAY DIFFRACTION64.96
2.16-2.20.33231100.23963015X-RAY DIFFRACTION69.97
2.2-2.240.25351280.24353318X-RAY DIFFRACTION78.46
2.24-2.290.24841470.23813725X-RAY DIFFRACTION86.08
2.29-2.340.26181560.23724013X-RAY DIFFRACTION93.5
2.34-2.390.29251570.2424152X-RAY DIFFRACTION97.8
2.39-2.450.27221550.2414246X-RAY DIFFRACTION99.73
2.45-2.520.23271660.23564275X-RAY DIFFRACTION99.71
2.52-2.590.31191580.22744260X-RAY DIFFRACTION99.64
2.59-2.670.23771630.22914287X-RAY DIFFRACTION99.75
2.67-2.770.26431580.22224265X-RAY DIFFRACTION99.86
2.77-2.880.24381590.2224294X-RAY DIFFRACTION99.8
2.88-3.010.23391570.21374272X-RAY DIFFRACTION99.86
3.01-3.170.20381630.20654286X-RAY DIFFRACTION99.82
3.17-3.370.22971570.2014266X-RAY DIFFRACTION99.95
3.37-3.630.17581600.18894331X-RAY DIFFRACTION99.93
3.63-3.990.17451570.17694261X-RAY DIFFRACTION99.95
3.99-4.570.17541600.16334265X-RAY DIFFRACTION99.91
4.57-5.760.13751660.16854269X-RAY DIFFRACTION99.69
5.76-46.980.18491540.20474258X-RAY DIFFRACTION99.28

+
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