[English] 日本語
Yorodumi
- PDB-6ii9: Crystal structure of H7 hemagglutinin from A/Anhui/1/2013 in comp... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ii9
TitleCrystal structure of H7 hemagglutinin from A/Anhui/1/2013 in complex with a human neutralizing antibody L3A-44
Components
  • (Hemagglutinin) x 2
  • Heavy chain of L3A-44 Fab
  • Light chain of L3A-44 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 / 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 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: 3.5 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 1.1Dec 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 1.2Feb 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
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 1.4Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Hemagglutinin
B: Hemagglutinin
C: Hemagglutinin
D: Hemagglutinin
E: Hemagglutinin
F: Hemagglutinin
H: Heavy chain of L3A-44 Fab
L: Light chain of L3A-44 Fab
M: Heavy chain of L3A-44 Fab
N: Light chain of L3A-44 Fab
P: Heavy chain of L3A-44 Fab
Q: Light chain of L3A-44 Fab
hetero molecules


Theoretical massNumber of molelcules
Total (without water)299,91715
Polymers299,25312
Non-polymers6643
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area47400 Å2
ΔGint-223 kcal/mol
Surface area109580 Å2
Unit cell
Length a, b, c (Å)178.457, 184.906, 188.990
Angle α, β, γ (deg.)90.00, 106.47, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Hemagglutinin / H7 Hemagglutinin


Mass: 34553.016 Da / Num. of mol.: 3
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: 19647.502 Da / Num. of mol.: 3
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 L3A-44 Fab


Mass: 23412.020 Da / Num. of mol.: 3
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 L3A-44 Fab


Mass: 22138.480 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm)
#5: 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.: 3
Source method: isolated from a genetically manipulated source
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
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 5 Å3/Da / Density % sol: 75.39 %
Crystal growTemperature: 291.15 K / Method: evaporation / pH: 7.5
Details: 0.2M Magnesium chloride hexahydrate, 0.1M HEPES pH 7.5, 22% w/v poly (acrylic acid sodium salt) 5100

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3.5→50 Å / Num. obs: 73039 / % possible obs: 98 % / Redundancy: 4.1 % / Biso Wilson estimate: 77.9 Å2 / CC1/2: 0.977 / Rpim(I) all: 0.111 / Rsym value: 0.199 / Net I/σ(I): 8.4
Reflection shellResolution: 3.5→3.63 Å / Mean I/σ(I) obs: 1.6

-
Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 3.5→43.841 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.64
RfactorNum. reflection% reflection
Rfree0.2338 3688 5.06 %
Rwork0.2007 --
obs0.2024 72894 96.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.5→43.841 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20897 0 42 0 20939
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00621431
X-RAY DIFFRACTIONf_angle_d0.99429116
X-RAY DIFFRACTIONf_dihedral_angle_d17.4317792
X-RAY DIFFRACTIONf_chiral_restr0.0523204
X-RAY DIFFRACTIONf_plane_restr0.0063791
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4814-3.52720.3908970.32861990X-RAY DIFFRACTION73
3.5272-3.57550.35611370.32112745X-RAY DIFFRACTION99
3.5755-3.62660.29841460.3062699X-RAY DIFFRACTION99
3.6266-3.68070.34981380.30032698X-RAY DIFFRACTION99
3.6807-3.73810.33591620.29042670X-RAY DIFFRACTION99
3.7381-3.79940.3161590.27812688X-RAY DIFFRACTION99
3.7994-3.86490.40761420.27652690X-RAY DIFFRACTION98
3.8649-3.93510.29921360.2722724X-RAY DIFFRACTION99
3.9351-4.01070.30361540.24982716X-RAY DIFFRACTION99
4.0107-4.09250.27541360.23752656X-RAY DIFFRACTION99
4.0925-4.18150.26271580.22122693X-RAY DIFFRACTION99
4.1815-4.27870.24831310.19892746X-RAY DIFFRACTION99
4.2787-4.38560.2311570.19162657X-RAY DIFFRACTION98
4.3856-4.5040.2061400.18012701X-RAY DIFFRACTION98
4.504-4.63640.21081470.1752693X-RAY DIFFRACTION98
4.6364-4.78590.18921550.16282691X-RAY DIFFRACTION98
4.7859-4.95670.17621330.16052717X-RAY DIFFRACTION98
4.9567-5.15490.21440.15832682X-RAY DIFFRACTION98
5.1549-5.38910.19171270.16332708X-RAY DIFFRACTION98
5.3891-5.67270.23081470.17732669X-RAY DIFFRACTION98
5.6727-6.02720.24661560.17512678X-RAY DIFFRACTION98
6.0272-6.49120.19041200.18332694X-RAY DIFFRACTION97
6.4912-7.1420.21391390.18682715X-RAY DIFFRACTION97
7.142-8.16960.20061470.16672624X-RAY DIFFRACTION96
8.1696-10.2710.14881310.13632700X-RAY DIFFRACTION97
10.271-43.84480.18731490.18562562X-RAY DIFFRACTION91
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.63580.12510.23920.01590.06460.26280.12970.23220.03720.0838-0.03140.02640.09720.0923-00.60260.0110.02190.60670.01540.606510.8084-65.426831.4965
20.1173-0.03130.12150.26250.29470.3905-0.10990.19380.13650.0207-0.0041-0.0537-0.0059-0.1643-00.3957-0.06930.00550.81890.05340.4252-34.8478-66.25546.821
30.32690.08130.2258-0.0556-0.03130.53680.2202-0.0819-0.1952-0.0128-0.0562-0.07510.262-0.2204-0.02570.5364-0.06770.02420.4030.00990.4247-6.141-83.363452.4191
40.57510.48430.05490.58650.2990.2570.2236-0.0257-0.04540.1905-0.0280.07630.2702-0.46220.19680.3319-0.1440.05670.93260.06930.4248-46.9515-74.041122.6737
50.61620.06650.4690.1780.12620.5466-0.07450.01680.13850.0334-0.04260.0558-0.0852-0.145800.56120.01930.04860.47840.00120.5487-5.9447-50.537355.5748
60.20050.1478-0.04860.1633-0.03370.0512-0.004-0.07020.2082-0.0294-0.05350.0357-0.1411-0.369300.510.1735-0.07860.9069-0.00610.5999-44.2338-52.951920.5692
70.25810.0042-0.06730.1481-0.12760.11520.22980.4039-0.06460.1508-0.2297-0.07420.02410.2057-0.00020.46580.1346-0.01960.8876-0.11050.499157.136-76.055538.9721
80.3636-0.0299-0.07350.0718-0.10050.16360.23981.0323-0.48170.27520.2084-0.2640.18190.36210.0170.86590.2834-0.22641.0299-0.29311.209282.7646-106.133748.7953
90.15770.0168-0.13820.261-0.15980.19680.26950.2715-0.42150.095-0.12810.39820.1108-0.1834-00.72120.1251-0.0960.8414-0.28250.950744.6563-94.734742.4293
100.26310.0368-0.15410.1526-0.13040.17760.2808-0.0088-0.30270.3798-0.20650.0873-0.17420.067300.89570.0756-0.13610.8891-0.14721.136668.7061-103.657257.2298
110.2509-0.0407-0.02880.1344-0.22270.39120.1459-0.0479-0.1297-0.2574-0.0095-0.00410.3263-0.055600.6867-0.0407-0.03610.440.10150.69318.9868-98.454190.5396
120.1731-0.1287-0.05670.2185-0.02510.160.2747-0.7964-0.5207-0.079-0.0577-0.0149-0.0082-0.41380.00950.7694-0.09510.02531.4290.13840.678823.7498-92.185130.2106
130.2360.00360.00530.43580.07470.3677-0.0091-0.06130.2153-0.1608-0.0374-0.1452-0.276-0.2243-00.5639-0.01060.03210.63930.06350.61885.9452-80.772296.02
140.06980.0258-0.10340.1919-0.04850.1450.4029-0.44420.2606-0.044-0.4126-0.0901-0.1739-0.2884-00.8466-0.07070.09021.16030.00310.963423.8439-78.4138120.5839
150.26390.27250.01030.27350.07810.4276-0.1498-0.16420.25540.0095-0.0070.15760.0066-0.0274-00.69050.0349-0.04660.3889-0.04610.690626.7657-28.412982.3675
160.33870.1070.17230.25240.05470.3581-0.6279-0.04550.82050.33470.0382-0.1865-0.202-0.1347-0.06430.763-0.2356-0.2050.76910.18461.026360.2514-5.898979.1366
170.35770.0879-0.17960.2031-0.12230.2445-0.31680.38080.0859-0.17310.10280.1272-0.10340.0795-0.00280.778-0.1484-0.07910.3770.11230.602431.8439-27.076960.3709
180.15280.1135-0.02760.14190.05740.1097-0.40510.2630.39910.0964-0.045-0.17020.24140.474500.9519-0.118-0.03940.79660.16010.814758.8156-19.996970.5047
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1:317 )A1 - 317
2X-RAY DIFFRACTION2( CHAIN B AND RESID 1:170 )B1 - 170
3X-RAY DIFFRACTION3( CHAIN C AND RESID 1:317 )C1 - 317
4X-RAY DIFFRACTION4( CHAIN D AND RESID 1:170 )D1 - 170
5X-RAY DIFFRACTION5( CHAIN E AND RESID 1:316 )E1 - 316
6X-RAY DIFFRACTION6( CHAIN F AND RESID 1:170 )F1 - 170
7X-RAY DIFFRACTION7( CHAIN H AND RESID 2:127 )H2 - 127
8X-RAY DIFFRACTION8( CHAIN H AND RESID 128:222 )H128 - 222
9X-RAY DIFFRACTION9( CHAIN L AND RESID 3:118 )L3 - 118
10X-RAY DIFFRACTION10( CHAIN L AND RESID 119:214 )L119 - 214
11X-RAY DIFFRACTION11( CHAIN M AND RESID 2:127 )M2 - 127
12X-RAY DIFFRACTION12( CHAIN M AND RESID 128:222 )M128 - 222
13X-RAY DIFFRACTION13( CHAIN N AND RESID 3:118 )N3 - 118
14X-RAY DIFFRACTION14( CHAIN N AND RESID 119:214 )N119 - 214
15X-RAY DIFFRACTION15( CHAIN P AND RESID 2:127 )P2 - 127
16X-RAY DIFFRACTION16( CHAIN P AND RESID 128:222 )P128 - 222
17X-RAY DIFFRACTION17( CHAIN Q AND RESID 3:118 )Q3 - 118
18X-RAY DIFFRACTION18( CHAIN Q AND RESID 119:214 )Q119 - 214

+
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