[English] 日本語
Yorodumi
- PDB-6v48: The crystal structure of hemagglutinin from A/mallard/Gurjev/263/... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6v48
TitleThe crystal structure of hemagglutinin from A/mallard/Gurjev/263/1982 (H14N5)
Components
  • Hemagglutinin HA1 chain
  • Hemagglutinin HA2 chain
KeywordsVIRAL PROTEIN / Influenza / avian / H14
Function / homology
Function and homology information


viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / membrane => GO:0016020 / 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
Similarity search - Function
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 / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.004 Å
AuthorsYang, H. / Stevens, J.
CitationJournal: Heliyon / Year: 2020
Title: Molecular characterization and three-dimensional structures of avian H8, H11, H14, H15 and swine H4 influenza virus hemagglutinins
Authors: Yang, H. / Carney, P.J. / Chang, J. / Stevens, J.
History
DepositionNov 27, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2020Provider: 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 / 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_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _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_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 11, 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 / citation / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _citation.country ..._chem_comp.pdbx_synonyms / _citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Hemagglutinin HA1 chain
B: Hemagglutinin HA2 chain
C: Hemagglutinin HA1 chain
D: Hemagglutinin HA2 chain
E: Hemagglutinin HA1 chain
F: Hemagglutinin HA2 chain
G: Hemagglutinin HA1 chain
H: Hemagglutinin HA2 chain
I: Hemagglutinin HA1 chain
J: Hemagglutinin HA2 chain
K: Hemagglutinin HA1 chain
L: Hemagglutinin HA2 chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)354,57530
Polymers348,15512
Non-polymers6,42018
Water0
1
A: Hemagglutinin HA1 chain
B: Hemagglutinin HA2 chain
E: Hemagglutinin HA1 chain
F: Hemagglutinin HA2 chain
K: Hemagglutinin HA1 chain
L: Hemagglutinin HA2 chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)177,28715
Polymers174,0776
Non-polymers3,2109
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area35160 Å2
ΔGint-76 kcal/mol
Surface area58430 Å2
MethodPISA
2
C: Hemagglutinin HA1 chain
D: Hemagglutinin HA2 chain
hetero molecules

G: Hemagglutinin HA1 chain
H: Hemagglutinin HA2 chain
hetero molecules

I: Hemagglutinin HA1 chain
J: Hemagglutinin HA2 chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)177,28715
Polymers174,0776
Non-polymers3,2109
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_545-x+1/2,y-1/2,-z1
crystal symmetry operation4_555-x+1/2,y+1/2,-z1
Buried area35160 Å2
ΔGint-78 kcal/mol
Surface area58420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)174.665, 100.974, 236.075
Angle α, β, γ (deg.)90.000, 103.930, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain C
31chain E
41chain G
51chain I
61chain K
12chain B
22chain D
32chain F
42chain H
52chain J
62chain L

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYGLYGLYchain AAA9 - 32713 - 331
21GLYGLYGLYGLYchain CCC9 - 32713 - 331
31GLYGLYGLYGLYchain EEE9 - 32713 - 331
41GLYGLYGLYGLYchain GGG9 - 32713 - 331
51GLYGLYGLYGLYchain III9 - 32713 - 331
61GLYGLYGLYGLYchain KKK9 - 32713 - 331
12ALAALALYSLYSchain BBB5 - 1725 - 172
22ALAALALYSLYSchain DDD5 - 1725 - 172
32ALAALALYSLYSchain FFF5 - 1725 - 172
42ALAALALYSLYSchain HHH5 - 1725 - 172
52ALAALALYSLYSchain JJJ5 - 1725 - 172
62ALAALALYSLYSchain LLL5 - 1725 - 172

NCS ensembles :
ID
1
2

-
Components

#1: Protein
Hemagglutinin HA1 chain


Mass: 36407.820 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (strain A/Mallard/Gurjev/263/1982 H14N5)
Strain: A/Mallard/Gurjev/263/1982 H14N5 / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P26136
#2: Protein
Hemagglutinin HA2 chain


Mass: 21617.939 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (strain A/Mallard/Gurjev/263/1982 H14N5)
Strain: A/Mallard/Gurjev/263/1982 H14N5 / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P26136
#3: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 6
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
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.9 Å3/Da / Density % sol: 57.61 %
Crystal growTemperature: 293 K / Method: microbatch
Details: 0.2M Sodium cacodylate trihydrate pH5.5, 20% (w/v) PEG4000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 16, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 79098 / % possible obs: 99.9 % / Redundancy: 3.8 % / Rsym value: 0.116 / Net I/σ(I): 7.7
Reflection shellResolution: 3→3.11 Å / Num. unique obs: 3949 / Rsym value: 0.56

-
Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHASESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3EYJ

3eyj


Resolution: 3.004→45.11 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 28.05
RfactorNum. reflection% reflection
Rfree0.2602 3949 4.99 %
Rwork0.2242 --
obs0.226 79098 99.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 219.19 Å2 / Biso mean: 60.2983 Å2 / Biso min: 1.09 Å2
Refinement stepCycle: final / Resolution: 3.004→45.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22902 0 420 0 23322
Biso mean--80.31 --
Num. residues----2922
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5898X-RAY DIFFRACTION0.827TORSIONAL
12C5898X-RAY DIFFRACTION0.827TORSIONAL
13E5898X-RAY DIFFRACTION0.827TORSIONAL
14G5898X-RAY DIFFRACTION0.827TORSIONAL
15I5898X-RAY DIFFRACTION0.827TORSIONAL
16K5898X-RAY DIFFRACTION0.827TORSIONAL
21B3138X-RAY DIFFRACTION0.827TORSIONAL
22D3138X-RAY DIFFRACTION0.827TORSIONAL
23F3138X-RAY DIFFRACTION0.827TORSIONAL
24H3138X-RAY DIFFRACTION0.827TORSIONAL
25J3138X-RAY DIFFRACTION0.827TORSIONAL
26L3138X-RAY DIFFRACTION0.827TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.004-3.04020.33341080.3062216880
3.0402-3.07870.33061280.28582677100
3.0787-3.11920.30831480.28412691100
3.1192-3.16190.372990.29362741100
3.1619-3.20710.35451190.28022683100
3.2071-3.25490.31831340.25032789100
3.2549-3.30580.27951380.25852614100
3.3058-3.360.28781650.25982728100
3.36-3.41790.31951360.26342636100
3.4179-3.480.28761590.24932730100
3.48-3.54690.28841280.24482623100
3.5469-3.61930.26921540.2242734100
3.6193-3.69790.2331690.21822661100
3.6979-3.78390.20381310.21892694100
3.7839-3.87850.24041220.2012788100
3.8785-3.98330.25311510.21042632100
3.9833-4.10040.26261390.20622678100
4.1004-4.23270.20581660.19992727100
4.2327-4.38390.21791410.1862731100
4.3839-4.55920.24911550.19312647100
4.5592-4.76650.24441430.17832717100
4.7665-5.01750.24021420.18382724100
5.0175-5.33140.1861450.1852698100
5.3314-5.74230.25971680.20392656100
5.7423-6.31880.25881310.21282784100
6.3188-7.22990.26591560.21692737100
7.2299-9.09660.24151410.22122732100
8-9.10.27981330.246272996
Refinement TLS params.Method: refined / Origin x: 14.5013 Å / Origin y: -0.8205 Å / Origin z: 53.148 Å
111213212223313233
T-0.0007 Å20.0066 Å20.0026 Å2-0.0599 Å20.0025 Å2--0.0419 Å2
L0.0754 °20.019 °2-0.0092 °2-0.1252 °2-0.0309 °2--0.0244 °2
S0.0171 Å °-0.0783 Å °0.0117 Å °0.0802 Å °-0.0103 Å °0.0455 Å °-0.0231 Å °0.0248 Å °0.0015 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA9 - 327
2X-RAY DIFFRACTION1allA501 - 602
3X-RAY DIFFRACTION1allB5 - 172
4X-RAY DIFFRACTION1allB201 - 202
5X-RAY DIFFRACTION1allC9 - 327
6X-RAY DIFFRACTION1allC501 - 602
7X-RAY DIFFRACTION1allD5 - 172
8X-RAY DIFFRACTION1allD201 - 202
9X-RAY DIFFRACTION1allE9 - 327
10X-RAY DIFFRACTION1allE501 - 602
11X-RAY DIFFRACTION1allF5 - 172
12X-RAY DIFFRACTION1allF201 - 202
13X-RAY DIFFRACTION1allG9 - 327
14X-RAY DIFFRACTION1allG501 - 602
15X-RAY DIFFRACTION1allH5 - 172
16X-RAY DIFFRACTION1allH201 - 202
17X-RAY DIFFRACTION1allI9 - 327
18X-RAY DIFFRACTION1allI501 - 602
19X-RAY DIFFRACTION1allJ5 - 172
20X-RAY DIFFRACTION1allJ201 - 202
21X-RAY DIFFRACTION1allK9 - 327
22X-RAY DIFFRACTION1allK501 - 602
23X-RAY DIFFRACTION1allL5 - 172
24X-RAY DIFFRACTION1allL201 - 202

+
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