[English] 日本語
Yorodumi
- PDB-6ii4: Crystal structure of H7 hemagglutinin from A/Anhui/1/2013 in comp... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ii4
TitleCrystal structure of H7 hemagglutinin from A/Anhui/1/2013 in complex with a human neutralizing antibody L4A-14
Components
  • (Hemagglutinin) x 2
  • Heavy chain of L4A-14 Fab
  • Light chain of L4A-14 Fab
KeywordsIMMUNE SYSTEM / H7 haemagglutinin / receptor binding site / neutralizing antibody / protection in vivo
Function / homology
Function and homology information


viral budding from plasma membrane / 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 / virion membrane
Similarity search - Function
Hemagglutinin; Chain A, domain 2 / Hemagglutinin Chain A, Domain 2 / Hemagglutinin Ectodomain; Chain B - #10 / Hemagglutinin Ectodomain; Chain B / 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 ...Hemagglutinin; Chain A, domain 2 / Hemagglutinin Chain A, Domain 2 / Hemagglutinin Ectodomain; Chain B - #10 / Hemagglutinin Ectodomain; Chain B / 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
Hemagglutinin / Hemagglutinin
Similarity search - Component
Biological speciesInfluenza A virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.3 Å
AuthorsJiang, H.H. / Shi, Y. / Qi, J. / Gao, G.F.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China81621091 China
National Natural Science Foundation of China81622031 China
Chinese Academy of SciencesXDB29010000 China
CitationJournal: Nat Microbiol / Year: 2019
Title: Structure-function analysis of neutralizing antibodies to H7N9 influenza from naturally infected humans.
Authors: Huang, K.A. / Rijal, P. / Jiang, H. / Wang, B. / Schimanski, L. / Dong, T. / Liu, Y.M. / Chang, P. / Iqbal, M. / Wang, M.C. / Chen, Z. / Song, R. / Huang, C.C. / Yang, J.H. / Qi, J. / Lin, T. ...Authors: Huang, K.A. / Rijal, P. / Jiang, H. / Wang, B. / Schimanski, L. / Dong, T. / Liu, Y.M. / Chang, P. / Iqbal, M. / Wang, M.C. / Chen, Z. / Song, R. / Huang, C.C. / Yang, J.H. / Qi, J. / Lin, T.Y. / Li, A. / Powell, T.J. / Jan, J.T. / Ma, C. / Gao, G.F. / Shi, Y. / Townsend, A.R.
History
DepositionOct 3, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 24, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 21, 2018Group: Data collection / Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_oper_list
Item: _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.oper_expression
Revision 1.2Dec 12, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Feb 6, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Hemagglutinin
B: Hemagglutinin
C: Hemagglutinin
D: Hemagglutinin
E: Heavy chain of L4A-14 Fab
F: Light chain of L4A-14 Fab
H: Heavy chain of L4A-14 Fab
L: Light chain of L4A-14 Fab


Theoretical massNumber of molelcules
Total (without water)200,8398
Polymers200,8398
Non-polymers00
Water0
1
A: Hemagglutinin
B: Hemagglutinin
H: Heavy chain of L4A-14 Fab
L: Light chain of L4A-14 Fab

A: Hemagglutinin
B: Hemagglutinin
H: Heavy chain of L4A-14 Fab
L: Light chain of L4A-14 Fab

A: Hemagglutinin
B: Hemagglutinin
H: Heavy chain of L4A-14 Fab
L: Light chain of L4A-14 Fab


Theoretical massNumber of molelcules
Total (without water)301,25912
Polymers301,25912
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-y+2,x-y,z1
crystal symmetry operation3_775-x+y+2,-x+2,z1
2
C: Hemagglutinin
D: Hemagglutinin
E: Heavy chain of L4A-14 Fab
F: Light chain of L4A-14 Fab

C: Hemagglutinin
D: Hemagglutinin
E: Heavy chain of L4A-14 Fab
F: Light chain of L4A-14 Fab

C: Hemagglutinin
D: Hemagglutinin
E: Heavy chain of L4A-14 Fab
F: Light chain of L4A-14 Fab


Theoretical massNumber of molelcules
Total (without water)301,25912
Polymers301,25912
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_865-y+3,x-y+1,z1
crystal symmetry operation3_785-x+y+2,-x+3,z1
Unit cell
Length a, b, c (Å)127.484, 127.484, 429.649
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

-
Components

#1: Protein Hemagglutinin / / H7 Hemagglutinin


Mass: 34553.016 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Gene: HA / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A024CX39
#2: Protein Hemagglutinin / / H7 Hemagglutinin


Mass: 19273.064 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Gene: HA / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A0K1LUI9
#3: Antibody Heavy chain of L4A-14 Fab


Mass: 23813.516 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm)
#4: Antibody Light chain of L4A-14 Fab


Mass: 22780.010 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm)

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.35 Å3/Da / Density % sol: 63.23 %
Crystal growTemperature: 291.15 K / Method: evaporation / pH: 7
Details: 0.2M Ammonium citrate tribasic pH7.0, 20%, 30 w/v PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3.3→50 Å / Num. obs: 39511 / % possible obs: 99.9 % / Redundancy: 6 % / Biso Wilson estimate: 78.7 Å2 / CC1/2: 0.998 / Rpim(I) all: 0.055 / Rsym value: 0.123 / Net I/σ(I): 14.8
Reflection shellResolution: 3.3→3.42 Å

-
Processing

Software
NameVersionClassification
PHENIX(1.11.1-2575_1692: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 3.3→41.044 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 28.8
RfactorNum. reflection% reflectionSelection details
Rfree0.2762 1981 5.02 %Cross-validaCross-validation methodtion method
Rwork0.2267 ---
obs0.2292 39479 99.77 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.3→41.044 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14016 0 0 0 14016
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00214334
X-RAY DIFFRACTIONf_angle_d0.60719450
X-RAY DIFFRACTIONf_dihedral_angle_d16.3045252
X-RAY DIFFRACTIONf_chiral_restr0.0412124
X-RAY DIFFRACTIONf_plane_restr0.0042544
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2884-3.37060.32151530.29712629X-RAY DIFFRACTION99
3.3706-3.46170.31381380.27952670X-RAY DIFFRACTION100
3.4617-3.56350.31941360.27012708X-RAY DIFFRACTION100
3.5635-3.67840.28921500.25992672X-RAY DIFFRACTION100
3.6784-3.80980.27791580.2572645X-RAY DIFFRACTION100
3.8098-3.96220.32571510.24932703X-RAY DIFFRACTION100
3.9622-4.14240.27081250.23032696X-RAY DIFFRACTION100
4.1424-4.36050.28191440.20282664X-RAY DIFFRACTION100
4.3605-4.63340.23141400.19392677X-RAY DIFFRACTION100
4.6334-4.99060.23961360.19642683X-RAY DIFFRACTION100
4.9906-5.49170.24951540.20222707X-RAY DIFFRACTION100
5.4917-6.2840.30451440.23562676X-RAY DIFFRACTION100
6.284-7.90790.2831260.25062698X-RAY DIFFRACTION100
7.9079-41.04740.26531260.20722670X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.24360.0759-0.3891-0.13430.42244.34260.01570.02480.0343-0.0596-0.11220.0224-0.3775-0.6813-0.00020.4610.0529-0.00840.4729-0.0140.4846114.368288.9511-24.6138
2-0.0815-0.1265-0.50380.6944-0.45941.4104-0.03560.01690.0915-0.0551-0.05840.0772-0.721-0.4774-0.00860.4117-0.0367-0.01540.41720.09440.3443124.312185.977-73.8334
30.03260.1335-0.10710.46640.9632.4956-0.061-0.2147-0.21450.37620.0352-0.11070.09830.42850.0021.0090.0761-0.1040.76280.1240.6677134.3593128.298541.5443
4-0.233-0.22810.2742-0.7710.26920.32480.1561-0.3067-0.06090.25720.175-0.21760.69040.43130.00852.0302-0.1617-0.32892.03160.12780.7363136.9385138.167290.8222
52.32750.65260.12522.25580.90981.38530.0767-0.0434-0.31490.1224-0.03470.00530.64250.0057-00.7060.12560.05980.30830.02040.6456133.2084112.7294-8.4592
61.5473-0.2135-1.15240.66211.38052.6568-0.98260.53120.2777-2.05261.0345-0.72290.82441.48330.08431.9585-0.50090.28221.54130.02851.0778141.8854120.4601-47.5681
70.69240.84620.69661.71090.18511.6357-0.16690.2271-0.0017-0.0187-0.0139-0.3673-0.4580.489700.6041-0.02570.03520.60680.02370.9254142.4607133.2897-9.9162
80.1656-0.0326-0.3350.2637-0.49091.2114-1.2741.59230.648-1.29640.8927-0.0198-0.86790.72250.00211.5339-0.5023-0.16921.33530.26881.4208135.4096133.1259-39.6554
92.0617-0.04260.11521.76510.01591.644-0.1110.40010.0528-0.14180.52870.21990.9277-2.08590.06410.09880.72910.09070.6034-0.10240.4987100.849696.421225.309
101.44710.2343-1.23540.7001-0.50960.9504-0.04-1.61760.34650.52130.3206-0.0403-1.86940.19050.00681.26520.1823-0.01931.7815-0.30510.8994112.4495100.380364.2384
111.2908-0.1548-0.61740.8397-0.71192.6001-0.0706-0.10010.0850.0691-0.1734-0.2759-0.60240.3084-00.44690.0296-0.03420.2846-0.02410.5318123.41193.489727.0861
120.7892-0.21370.64690.29880.29151.64150.2187-1.6359-0.57570.3679-0.7218-0.4801-0.77550.6748-0.01220.7734-0.02970.0041.06390.28561.1712119.5687.819256.7428
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 317)
2X-RAY DIFFRACTION2chain 'B' and (resid 5 through 170 )
3X-RAY DIFFRACTION3chain 'C' and (resid 1 through 317 )
4X-RAY DIFFRACTION4chain 'D' and (resid 5 through 170 )
5X-RAY DIFFRACTION5chain 'E' and (resid 1 through 119 )
6X-RAY DIFFRACTION6chain 'E' and (resid 120 through 225 )
7X-RAY DIFFRACTION7chain 'F' and (resid 1 through 117 )
8X-RAY DIFFRACTION8chain 'F' and (resid 118 through 212 )
9X-RAY DIFFRACTION9chain 'H' and (resid 1 through 119 )
10X-RAY DIFFRACTION10chain 'H' and (resid 120 through 225 )
11X-RAY DIFFRACTION11chain 'L' and (resid 1 through 119 )
12X-RAY DIFFRACTION12chain 'L' and (resid 120 through 212 )

+
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