[English] 日本語
Yorodumi
- PDB-6a67: Crystal structure of influenza A virus H5 hemagglutinin globular ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6a67
TitleCrystal structure of influenza A virus H5 hemagglutinin globular head in complex with the Fab of antibody FLD21.140
Components
  • FLD21.140 Heavy Chain
  • FLD21.140 Light Chain
  • Hemagglutinin
KeywordsIMMUNE SYSTEM / influenza virus / H5N1 / neutralizing antibodies / receptor binding site
Function / homology
Function and homology information


clathrin-dependent endocytosis of virus by host cell / host cell surface receptor binding / apical plasma membrane / 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
Similarity search - Function
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 / Immunoglobulins / Alpha-Beta Complex / Immunoglobulin-like ...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 / Immunoglobulins / Alpha-Beta Complex / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Influenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.33 Å
AuthorsWang, P. / Zuo, Y. / Sun, J. / Zhang, L. / Wang, X.
Funding support China, 10items
OrganizationGrant numberCountry
National Natural Science Foundation of China81530065 China
National Natural Science Foundation of China81661128042 China
National Natural Science Foundation of China31470751 China
National Natural Science Foundation of ChinaU1405228 China
Ministry of Science and Technology (China)2016YFD0500307 China
Ministry of Science and Technology (China)2012ZX10001-004 China
Ministry of Science and Technology (China)2012ZX10001-006 China
Ministry of Science and Technology (China)2012ZX10001-009 China
Ministry of Science and Technology (China)2017ZX10201-101 China
Ministry of Science and Technology (China)2014CB542500-03 China
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Complementary recognition of the receptor-binding site of highly pathogenic H5N1 influenza viruses by two human neutralizing antibodies.
Authors: Zuo, Y. / Wang, P. / Sun, J. / Guo, S. / Wang, G. / Zuo, T. / Fan, S. / Zhou, P. / Liang, M. / Shi, X. / Wang, X. / Zhang, L.
History
DepositionJun 26, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 29, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 19, 2018Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 21, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
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_conn / 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 / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
H: FLD21.140 Heavy Chain
L: FLD21.140 Light Chain
C: FLD21.140 Heavy Chain
D: FLD21.140 Light Chain
B: Hemagglutinin
A: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,46210
Polymers146,5786
Non-polymers8854
Water7,440413
1
H: FLD21.140 Heavy Chain
L: FLD21.140 Light Chain
A: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,7315
Polymers73,2893
Non-polymers4422
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5270 Å2
ΔGint-23 kcal/mol
Surface area28270 Å2
MethodPISA
2
C: FLD21.140 Heavy Chain
D: FLD21.140 Light Chain
B: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,7315
Polymers73,2893
Non-polymers4422
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5170 Å2
ΔGint-24 kcal/mol
Surface area28340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)168.106, 168.106, 147.188
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number93
Space group name H-MP4222
Components on special symmetry positions
IDModelComponents
11D-381-

HOH

-
Components

#1: Antibody FLD21.140 Heavy Chain


Mass: 23979.801 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293T / Production host: Homo sapiens (human)
#2: Antibody FLD21.140 Light Chain


Mass: 22838.131 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293T / Production host: Homo sapiens (human)
#3: Protein Hemagglutinin


Mass: 26470.893 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/Thailand/1(KAN-1)/2004(H5N1))
Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q6Q794
#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.: 4
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 413 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.6 Å3/Da / Density % sol: 65.89 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / Details: 2.0M (NH4)2SO4. 0.1M Bis-Tris pH 5.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9796 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 13, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.33→50 Å / Num. obs: 89876 / % possible obs: 99.5 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 22.3
Reflection shellResolution: 2.33→2.37 Å / Rmerge(I) obs: 0.995 / Num. unique obs: 4350

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DUT

5dut


Resolution: 2.33→36.913 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.88
RfactorNum. reflection% reflection
Rfree0.2352 4414 4.91 %
Rwork0.1966 --
obs0.1985 89843 99.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.33→36.913 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9777 0 56 413 10246
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00910114
X-RAY DIFFRACTIONf_angle_d1.17113813
X-RAY DIFFRACTIONf_dihedral_angle_d14.6366010
X-RAY DIFFRACTIONf_chiral_restr0.0641549
X-RAY DIFFRACTIONf_plane_restr0.0071755
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3289-2.35530.32421550.26982708X-RAY DIFFRACTION97
2.3553-2.3830.30821280.25982816X-RAY DIFFRACTION99
2.383-2.41210.31551480.25752804X-RAY DIFFRACTION100
2.4121-2.44260.29431630.24942804X-RAY DIFFRACTION100
2.4426-2.47480.2741740.25512805X-RAY DIFFRACTION100
2.4748-2.50870.3621390.24652806X-RAY DIFFRACTION100
2.5087-2.54450.31251400.24962832X-RAY DIFFRACTION100
2.5445-2.58250.31541540.24742803X-RAY DIFFRACTION100
2.5825-2.62280.28381560.24242811X-RAY DIFFRACTION100
2.6228-2.66580.29661390.23352853X-RAY DIFFRACTION100
2.6658-2.71170.28361650.21912780X-RAY DIFFRACTION100
2.7117-2.7610.30921400.2322850X-RAY DIFFRACTION100
2.761-2.81410.28861270.22412824X-RAY DIFFRACTION100
2.8141-2.87150.28591560.22642836X-RAY DIFFRACTION100
2.8715-2.9340.29521460.21422834X-RAY DIFFRACTION100
2.934-3.00220.26251620.22422856X-RAY DIFFRACTION100
3.0022-3.07720.25451440.21632826X-RAY DIFFRACTION100
3.0772-3.16040.25451420.21462850X-RAY DIFFRACTION100
3.1604-3.25330.25321390.21262863X-RAY DIFFRACTION100
3.2533-3.35830.25251460.20282856X-RAY DIFFRACTION100
3.3583-3.47820.2221420.19432854X-RAY DIFFRACTION100
3.4782-3.61740.21591310.18982870X-RAY DIFFRACTION100
3.6174-3.78180.22441310.18062901X-RAY DIFFRACTION100
3.7818-3.9810.21211210.1712893X-RAY DIFFRACTION100
3.981-4.23010.18771390.15932888X-RAY DIFFRACTION100
4.2301-4.55610.1831480.14472886X-RAY DIFFRACTION100
4.5561-5.01360.18521710.14752873X-RAY DIFFRACTION100
5.0136-5.73680.18621630.1732924X-RAY DIFFRACTION100
5.7368-7.21890.25311540.21012943X-RAY DIFFRACTION99
7.2189-36.91770.21251510.21172980X-RAY DIFFRACTION95
Refinement TLS params.Method: refined / Origin x: 353.3282 Å / Origin y: -114.1824 Å / Origin z: 159.4992 Å
111213212223313233
T0.2752 Å2-0.0059 Å2-0.026 Å2-0.2821 Å2-0.002 Å2--0.308 Å2
L0.0862 °2-0.0386 °2-0.1197 °2-0.1393 °20.0459 °2--0.2642 °2
S0.0209 Å °0.012 Å °-0.0347 Å °-0.0207 Å °-0.014 Å °0.0394 Å °0.0179 Å °-0.0311 Å °-0.0155 Å °
Refinement TLS groupSelection details: all

+
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