[English] 日本語
Yorodumi
- PDB-6n5d: Broadly protective antibodies directed to a subdominant influenza... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6n5d
TitleBroadly protective antibodies directed to a subdominant influenza hemagglutinin epitope
Components
  • Hemagglutinin
  • antibody heavy chain
  • antibody light chain
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / influenza / antibody / complex / hemagglutinin / immunogen design / glycan / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / membrane
Similarity search - Function
Hemagglutinin; Chain A, domain 2 / Hemagglutinin Chain A, Domain 2 / Hemagglutinin (Ha1 Chain); Chain: A; domain 1 / Haemagglutinin, alpha/beta domain, HA1 chain / Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B / Viral capsid/haemagglutinin protein / Ribbon ...Hemagglutinin; Chain A, domain 2 / Hemagglutinin Chain A, Domain 2 / Hemagglutinin (Ha1 Chain); Chain: A; domain 1 / Haemagglutinin, alpha/beta domain, HA1 chain / Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B / Viral capsid/haemagglutinin protein / Ribbon / Immunoglobulins / Alpha-Beta Complex / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesInfluenza A virus
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsBajic, G. / Schmidt, A.G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P01 AI089618 United States
CitationJournal: Cell Host Microbe / Year: 2019
Title: Influenza Antigen Engineering Focuses Immune Responses to a Subdominant but Broadly Protective Viral Epitope.
Authors: Bajic, G. / Maron, M.J. / Adachi, Y. / Onodera, T. / McCarthy, K.R. / McGee, C.E. / Sempowski, G.D. / Takahashi, Y. / Kelsoe, G. / Kuraoka, M. / Schmidt, A.G.
History
DepositionNov 21, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2019Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Hemagglutinin
C: antibody heavy chain
B: Hemagglutinin
E: antibody heavy chain
K: Hemagglutinin
L: antibody heavy chain
N: antibody light chain
F: antibody light chain
D: antibody light chain


Theoretical massNumber of molelcules
Total (without water)238,2249
Polymers238,2249
Non-polymers00
Water00
1
A: Hemagglutinin
C: antibody heavy chain
D: antibody light chain


Theoretical massNumber of molelcules
Total (without water)79,4083
Polymers79,4083
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4950 Å2
ΔGint-30 kcal/mol
Surface area32040 Å2
MethodPISA
2
B: Hemagglutinin
E: antibody heavy chain
F: antibody light chain


Theoretical massNumber of molelcules
Total (without water)79,4083
Polymers79,4083
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4960 Å2
ΔGint-31 kcal/mol
Surface area32010 Å2
MethodPISA
3
K: Hemagglutinin
L: antibody heavy chain
N: antibody light chain


Theoretical massNumber of molelcules
Total (without water)79,4083
Polymers79,4083
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5170 Å2
ΔGint-28 kcal/mol
Surface area32120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)153.190, 153.190, 94.160
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31

-
Components

#1: Protein Hemagglutinin


Mass: 31150.033 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P03437
#2: Antibody antibody heavy chain


Mass: 25338.352 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: HC / Production host: Homo sapiens (human)
#3: Antibody antibody light chain


Mass: 22919.457 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.74 Å3/Da / Density % sol: 55.13 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2 M sodium bromide, 0.1 M Bis-Tris propane, pH 6.5, 20% w/v PEG3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9787 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 23, 2018
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
Reflection twinOperator: -k,-h,-l / Fraction: 0.46
ReflectionResolution: 3→44.369 Å / Num. obs: 49440 / % possible obs: 100 % / Redundancy: 6.437 % / Biso Wilson estimate: 51.897 Å2 / CC1/2: 0.985 / Rmerge(I) obs: 0.255 / Rrim(I) all: 0.277 / Χ2: 0.914 / Net I/σ(I): 9.22 / Num. measured all: 318259 / Scaling rejects: 5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
3-3.36.451.1991.84122680.4551.304100
3.3-3.56.4430.6483.4260140.7090.705100
3.5-46.4310.3845.64103010.8720.417100
4-56.4010.16112.44102020.9790.175100
5-66.3340.14513.444770.9830.158100
6-106.5780.08421.548600.9970.091100
10-206.520.03247.311670.9990.035100
20-306.1540.03154.121170.9990.034100
30-505.2940.02353.03340.9990.02694.4
44.369-500

-
Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XSCALEdata scaling
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 1HA0, 6N5B, & 4HKX

1ha0

6n5b

4hkx


Resolution: 3→44.369 Å / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 23.82
RfactorNum. reflection% reflection
Rfree0.2444 2396 4.85 %
Rwork0.2173 --
obs0.2279 49440 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 127.15 Å2 / Biso mean: 55.5971 Å2 / Biso min: 26.59 Å2
Refinement stepCycle: final / Resolution: 3→44.369 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16356 0 0 0 16356
Num. residues----2148
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.001-3.06220.35271480.30852742289095
3.0622-3.12870.3267980.28852812291097
3.1287-3.20140.32291580.28972743290195
3.2014-3.28140.2941600.28362739289994
3.2814-3.370.26911700.26312716288694
3.37-3.4690.2671200.25792805292596
3.469-3.58070.30621300.25332751288195
3.5807-3.70850.30451580.24212737289595
3.7085-3.85660.26341760.23642746292294
3.8566-4.03170.22711180.23042790290896
4.0317-4.24370.23361420.20882741288395
4.2437-4.50860.20951440.2012803294795
4.5086-4.85520.20771450.17692762290795
4.8552-5.34110.24621300.18632743287395
5.3411-6.10770.2331240.19432758288296
6.1077-7.67130.21271200.20362804292496
7.6713-28.99260.24431550.23452758291395

+
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