[English] 日本語
Yorodumi
- PDB-6n5b: Broadly protective antibodies directed to a subdominant influenza... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6n5b
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 / homologyHemagglutinin (Ha1 Chain); Chain: A; domain 1 / Haemagglutinin, alpha/beta domain, HA1 chain / Immunoglobulins / Alpha-Beta Complex / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta / 2-acetamido-2-deoxy-beta-D-galactopyranose
Function and homology information
Biological speciesMus musculus (house mouse)
Influenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.5 Å
AuthorsBajic, G. / Maron, M.J. / 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 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
H: antibody heavy chain
L: antibody light chain
B: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,6904
Polymers71,4693
Non-polymers2211
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5740 Å2
ΔGint-30 kcal/mol
Surface area28070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.002, 124.002, 90.090
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

-
Components

#1: Antibody antibody heavy chain


Mass: 24139.053 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#2: Antibody antibody light chain


Mass: 22637.074 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#3: Protein Hemagglutinin


Mass: 24692.602 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Gene: HA / Production host: Trichoplusia ni (cabbage looper)
#4: Sugar ChemComp-NGA / 2-acetamido-2-deoxy-beta-D-galactopyranose


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGalpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-galactopyranosamineCOMMON NAMEGMML 1.0
b-D-GalpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.8 Å3/Da / Density % sol: 56.03 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1 M MES, pH 6.5, 12% PEG20000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9792 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: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3→46.124 Å / Num. obs: 10398 / % possible obs: 98.8 % / Redundancy: 5.158 % / Biso Wilson estimate: 114.572 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.156 / Rrim(I) all: 0.174 / Χ2: 1.025 / Net I/σ(I): 6.1 / Num. measured all: 83144 / Scaling rejects: 7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible allCC1/2
3-3.085.2196.1460.136080118211656.84998.6
3.08-3.175.3854.3850.236203115511524.87399.7
3.17-3.265.2782.770.456038114811443.08599.70.142
3.26-3.365.2192.2030.595657109010842.45999.40.16
3.36-3.475.1011.4580.945422106810631.6399.50.363
3.47-3.594.8671.0571.324925101710121.18799.50.524
3.59-3.724.9240.8341.73487510019900.93598.90.574
3.72-3.885.3720.6552.4450609509420.72799.20.723
3.88-4.055.3620.4673.3849289259190.51999.40.863
4.05-4.255.270.295.2646438888810.32399.20.94
4.25-4.485.2820.2176.8844328488390.24198.90.968
4.48-4.755.1580.1589.2940497967850.17698.60.977
4.75-5.084.970.13910.2136787477400.15699.10.982
5.08-5.484.6980.11611.1232326996880.1398.40.986
5.48-6.015.230.11512.333216506350.12897.70.986
6.01-6.715.3960.09614.3431465925830.10698.50.992
6.71-7.755.3280.0718.327495285160.07897.70.996
7.75-9.54.880.04725.3321574534420.05397.60.998
9.5-13.434.6790.03731.0415913573400.04295.20.998
13.43-46.1244.8140.02835.129582151990.03292.60.999

-
Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementResolution: 3.5→46.124 Å / SU ML: 0.52 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 34.63
RfactorNum. reflection% reflection
Rfree0.2784 540 5.27 %
Rwork0.2355 --
obs0.2377 10239 98.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 274.04 Å2 / Biso mean: 134.9668 Å2 / Biso min: 82.11 Å2
Refinement stepCycle: final / Resolution: 3.5→46.124 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5029 0 14 0 5043
Biso mean--154.21 --
Num. residues----654
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.5001-3.85220.38631340.31342397253199
3.8522-4.40920.30651280.24522416254499
4.4092-5.55360.26311430.21412399254299
5.5536-46.12760.25671350.22782487262297
Refinement TLS params.Method: refined / Origin x: 207.0924 Å / Origin y: 208.4011 Å / Origin z: 0.0458 Å
111213212223313233
T1.1461 Å2-0.0288 Å20.059 Å2-0.9706 Å20.11 Å2--0.9159 Å2
L2.3893 °2-2.4562 °2-1.0178 °2-3.946 °21.598 °2--0.9659 °2
S0.2808 Å °-0.0546 Å °0.147 Å °-0.3538 Å °-0.0556 Å °-0.2142 Å °0.0216 Å °-0.0177 Å °-0.2221 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allH1 - 218
2X-RAY DIFFRACTION1allL1 - 211
3X-RAY DIFFRACTION1allB51 - 301

+
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://pdbjlvh1.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