[English] 日本語
Yorodumi
- PDB-4lkk: The structure of hemagglutinin L226Q mutant (H3 numbering) from a... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4lkk
TitleThe structure of hemagglutinin L226Q mutant (H3 numbering) from a avian-origin H7N9 influenza virus (A/Anhui/1/2013) in complex with human receptor analog 6'SLNLN
Components(hemagglutinin) x 2
KeywordsVIRAL PROTEIN / homotrimer / virus attachment / membrane fusion
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
Haemagglutinin, influenzavirus 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 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 / Alpha-Beta Complex / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Hemagglutinin / Hemagglutinin
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.491 Å
AuthorsShi, Y. / Zhang, W. / Wang, F. / Qi, J. / Song, H. / Wu, Y. / Gao, F. / Zhang, Y. / Fan, Z. / Gong, W. ...Shi, Y. / Zhang, W. / Wang, F. / Qi, J. / Song, H. / Wu, Y. / Gao, F. / Zhang, Y. / Fan, Z. / Gong, W. / Wang, D. / Shu, Y. / Wang, Y. / Yan, J. / Gao, G.F.
CitationJournal: Science / Year: 2013
Title: Structures and receptor binding of hemagglutinins from human-infecting H7N9 influenza viruses
Authors: Shi, Y. / Zhang, W. / Wang, F. / Qi, J. / Wu, Y. / Song, H. / Gao, F. / Bi, Y. / Zhang, Y. / Fan, Z. / Qin, C. / Sun, H. / Liu, J. / Haywood, J. / Liu, W. / Gong, W. / Wang, D. / Shu, Y. / ...Authors: Shi, Y. / Zhang, W. / Wang, F. / Qi, J. / Wu, Y. / Song, H. / Gao, F. / Bi, Y. / Zhang, Y. / Fan, Z. / Qin, C. / Sun, H. / Liu, J. / Haywood, J. / Liu, W. / Gong, W. / Wang, D. / Shu, Y. / Wang, Y. / Yan, J. / Gao, G.F.
History
DepositionJul 7, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 6, 2013Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_special_symmetry / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 8, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: hemagglutinin
B: hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,7796
Polymers53,6442
Non-polymers1,1354
Water2,036113
1
A: hemagglutinin
B: hemagglutinin
hetero molecules

A: hemagglutinin
B: hemagglutinin
hetero molecules

A: hemagglutinin
B: hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)164,33718
Polymers160,9316
Non-polymers3,40512
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area36170 Å2
ΔGint-119 kcal/mol
Surface area56920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.143, 117.143, 297.664
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-730-

HOH

21A-740-

HOH

31B-601-

HOH

41B-623-

HOH

51B-630-

HOH

61B-632-

HOH

71B-634-

HOH

-
Components

#1: Protein hemagglutinin


Mass: 34210.562 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Anhui/1/2013 / Plasmid: pFastbac1 / Cell line (production host): HI5 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: V5IRV5*PLUS
#2: Protein hemagglutinin


Mass: 19433.254 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Anhui/1/2013 / Plasmid: pFastbac1 / Cell line (production host): HI5 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: V5IRV2*PLUS
#3: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose


Type: oligosaccharide / Mass: 471.411 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Aca2-6DGalpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O]/1-2/a6-b2WURCSPDB2Glycan 1.1.0
[][b-D-Galp]{[(6+2)][a-D-Neup5Ac]{}}LINUCSPDB-CARE
#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.: 3
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.: 113 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE DATABASE REFERENCES FOR THIS PROTEIN WHICH DERIVED FROM STRAIN A/ANHUI/1/2013 DOES NOT ...THE SEQUENCE DATABASE REFERENCES FOR THIS PROTEIN WHICH DERIVED FROM STRAIN A/ANHUI/1/2013 DOES NOT CURRENTLY EXIST.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.66 Å3/Da / Density % sol: 66.43 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 16%(w/v) Polyethylene glycol 3350, 0.2M lithium sulfate, 0.1M Tris, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 28, 2013
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.491→50 Å / Num. all: 27839 / Num. obs: 27271 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 56.96 Å2
Reflection shellResolution: 2.5→2.59 Å / % possible all: 99.6

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DJ6

4dj6


Resolution: 2.491→48.013 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7839 / SU ML: 0.41 / σ(F): 1.34 / Phase error: 28.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.271 1363 5 %RANDOM
Rwork0.2361 ---
all0.2379 27268 --
obs0.2379 27268 97.65 %-
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.365 Å2 / ksol: 0.297 e/Å3
Displacement parametersBiso max: 180.79 Å2 / Biso mean: 75.3171 Å2 / Biso min: 30.79 Å2
Baniso -1Baniso -2Baniso -3
1-2.9833 Å20 Å20 Å2
2--2.9833 Å2-0 Å2
3----5.9666 Å2
Refinement stepCycle: LAST / Resolution: 2.491→48.013 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3760 0 74 113 3947
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073914
X-RAY DIFFRACTIONf_angle_d0.9935284
X-RAY DIFFRACTIONf_chiral_restr0.201580
X-RAY DIFFRACTIONf_plane_restr0.004693
X-RAY DIFFRACTIONf_dihedral_angle_d19.2921446
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4907-2.57970.37861150.34042544265997
2.5797-2.6830.36631350.315825912726100
2.683-2.80510.33731410.312726262767100
2.8051-2.9530.35481450.281925832728100
2.953-3.1380.33531400.27112611275199
3.138-3.38020.32421350.27192627276299
3.3802-3.72020.27881490.23892589273899
3.7202-4.25830.22731490.212555270497
4.2583-5.36380.21621390.18572561270095
5.3638-48.02140.23921150.22142618273393
Refinement TLS params.Method: refined / Origin x: -15.8159 Å / Origin y: 3.9028 Å / Origin z: 56.8673 Å
111213212223313233
T0.3067 Å20.0055 Å20.0391 Å2-0.3397 Å2-0.0268 Å2--0.4367 Å2
L0.8419 °2-0.0731 °20.158 °2-0.9992 °2-0.376 °2--1.2263 °2
S0.0462 Å °-0.2008 Å °0.0135 Å °0.0748 Å °0.0142 Å °0.0768 Å °0.0514 Å °-0.1283 Å °-0.0508 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://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