[English] 日本語
Yorodumi
- PDB-5ugy: Influenza hemagglutinin in complex with a neutralizing antibody -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ugy
TitleInfluenza hemagglutinin in complex with a neutralizing antibody
Components
  • (Hemagglutinin ...) x 2
  • CH65 heavy chain
  • CH65 light chain
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / influenza hemagglutinin / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


immunoglobulin complex / viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / adaptive immune response / 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 ...immunoglobulin complex / viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / adaptive immune response / 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 / extracellular region / membrane / plasma 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 ...: / 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 / Immunoglobulin V-Type / Immunoglobulin V-set domain / Ribbon / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Alpha-Beta Complex / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Hemagglutinin / Hemagglutinin / Hemagglutinin / IGL@ protein / IgG H chain
Similarity search - Component
Biological speciesInfluenza A virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.801 Å
AuthorsWhittle, J.R.R. / Jenni, S. / Harrison, S.C.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2011
Title: Broadly neutralizing human antibody that recognizes the receptor-binding pocket of influenza virus hemagglutinin.
Authors: Whittle, J.R. / Zhang, R. / Khurana, S. / King, L.R. / Manischewitz, J. / Golding, H. / Dormitzer, P.R. / Haynes, B.F. / Walter, E.B. / Moody, M.A. / Kepler, T.B. / Liao, H.X. / Harrison, S.C.
History
DepositionJan 10, 2017Deposition site: RCSB / Processing site: RCSB
SupersessionJan 25, 2017ID: 3SM5
Revision 1.0Jan 25, 2017Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / 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_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 / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _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.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 2.1Oct 4, 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 2.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Hemagglutinin HA1
B: Hemagglutinin HA2
C: Hemagglutinin HA1
D: Hemagglutinin HA2
E: Hemagglutinin HA1
F: Hemagglutinin HA2
H: CH65 heavy chain
I: CH65 heavy chain
J: CH65 heavy chain
L: CH65 light chain
M: CH65 light chain
N: CH65 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)313,20927
Polymers307,57612
Non-polymers5,63315
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area52610 Å2
ΔGint-164 kcal/mol
Surface area119270 Å2
Unit cell
Length a, b, c (Å)154.824, 192.190, 333.219
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number24
Space group name H-MI212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain N
21chain L
31chain M
12chain A
22chain C
32chain E
13chain B
23chain D
33chain F
14chain J
24chain H
34chain I

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain NN2 - 211
211chain LL2 - 211
311chain MM2 - 211
112chain AA4 - 8290
212chain CC4 - 8290
312chain EE4 - 8290
113chain BB501 - 673
213chain DD501 - 673
313chain FF501 - 673
114chain JJ1 - 227
214chain HH1 - 227
314chain II1 - 227

NCS ensembles :
ID
1
2
3
4

-
Components

-
Hemagglutinin ... , 2 types, 6 molecules ACEBDF

#1: Protein Hemagglutinin HA1


Mass: 36024.344 Da / Num. of mol.: 3 / Fragment: UNP residues 18-339
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/Solomon Islands/3/2006(H1N1))
Strain: A/Solomon Islands/3/2006(H1N1) / Gene: HA / Plasmid: pFastBac / Cell line (production host): HI-5 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A7UPX0, UniProt: A7Y8A6*PLUS
#2: Protein Hemagglutinin HA2


Mass: 19841.041 Da / Num. of mol.: 3 / Fragment: UNP residues 344-516
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/Solomon Islands/3/2006(H1N1))
Strain: A/Solomon Islands/3/2006(H1N1) / Gene: HA / Plasmid: pFastBac / Cell line (production host): HI-5 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A7UPX0, UniProt: A7Y8I1*PLUS

-
Antibody , 2 types, 6 molecules HIJLMN

#3: Antibody CH65 heavy chain


Mass: 24387.211 Da / Num. of mol.: 3 / Fragment: Fab
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: S6C4S0
#4: Antibody CH65 light chain


Mass: 22272.625 Da / Num. of mol.: 3 / Fragment: Fab
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGL@ / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: Q8N355

-
Sugars , 3 types, 15 molecules

#5: 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.: 6
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
#6: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#7: 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.: 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

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.05 Å3/Da / Density % sol: 69.64 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 2.2 M ammonium sulfate, 100 mM Tris, 5% PEG400, pH 7.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.987 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 18, 2011
RadiationMonochromator: Cryogenically-cooled single crystal Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.8→29.923 Å / Num. obs: 114569 / % possible obs: 94 % / Observed criterion σ(I): -3 / Redundancy: 5.702 % / Biso Wilson estimate: 40 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.145 / Rrim(I) all: 0.159 / Χ2: 0.997 / Net I/σ(I): 11.09 / Num. measured all: 653278 / Scaling rejects: 2338
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.8-2.873.8215.5760.3163560.1316.40970.9
2.87-2.954.343.1430.565940.2133.55776.2
2.95-3.044.6572.3760.7169190.2972.66981.5
3.04-3.134.9441.7241.0373690.4731.92289.5
3.13-3.235.3711.051.7479070.6711.16398.7
3.23-3.356.0610.7232.7477370.8280.79299.8
3.35-3.476.2940.4854.174390.9250.5399.9
3.47-3.616.3010.3455.8271710.9560.376100
3.61-3.786.2670.2557.7569270.9730.27899.9
3.78-3.966.2660.29.5765870.9860.21899.9
3.96-4.176.2390.14213.1863150.9910.155100
4.17-4.436.2260.10616.7659330.9950.11599.9
4.43-4.736.2050.08220.7856080.9970.0999.9
4.73-5.116.2090.07622.2652320.9970.08399.9
5.11-5.66.1730.07123.2248570.9970.07799.9
5.6-6.266.1260.0723.3243650.9970.077100
6.26-7.236.0110.06226.3638730.9970.06899.8
7.23-8.855.7990.04333.9633160.9980.04799.8
8.85-12.525.7760.0345.6225950.9990.03399.8
12.52-29.9235.3320.02844.9114690.9990.03196.8

-
Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1RVZ

1rvz


Resolution: 2.801→29.923 Å / SU ML: 0.54 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 32.74
RfactorNum. reflection% reflection
Rfree0.2888 2752 2.47 %
Rwork0.2591 --
obs0.2598 111548 91.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 176.94 Å2 / Biso mean: 49.1023 Å2 / Biso min: 3.52 Å2
Refinement stepCycle: final / Resolution: 2.801→29.923 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21513 0 723 0 22236
Biso mean--102.57 --
Num. residues----2781
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00322467
X-RAY DIFFRACTIONf_angle_d0.68530618
X-RAY DIFFRACTIONf_chiral_restr0.0473402
X-RAY DIFFRACTIONf_plane_restr0.0073936
X-RAY DIFFRACTIONf_dihedral_angle_d7.20917982
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11N3612X-RAY DIFFRACTION2.508TORSIONAL
12L3612X-RAY DIFFRACTION2.508TORSIONAL
13M3612X-RAY DIFFRACTION2.508TORSIONAL
21A6161X-RAY DIFFRACTION2.508TORSIONAL
22C6161X-RAY DIFFRACTION2.508TORSIONAL
23E6161X-RAY DIFFRACTION2.508TORSIONAL
31B3268X-RAY DIFFRACTION2.508TORSIONAL
32D3268X-RAY DIFFRACTION2.508TORSIONAL
33F3268X-RAY DIFFRACTION2.508TORSIONAL
41J3903X-RAY DIFFRACTION2.508TORSIONAL
42H3903X-RAY DIFFRACTION2.508TORSIONAL
43I3903X-RAY DIFFRACTION2.508TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8006-2.84890.4203630.39852274233739
2.8489-2.90060.3969940.38573788388264
2.9006-2.95640.3981000.38874366446674
2.9564-3.01660.38081350.37944635477079
3.0166-3.08220.40981150.38735033514885
3.0822-3.15380.44371380.35635493563193
3.1538-3.23260.41491450.345869601499
3.2326-3.31990.35741670.321658636030100
3.3199-3.41740.36421370.312858726009100
3.4174-3.52760.32751530.285959386091100
3.5276-3.65340.28311580.260358776035100
3.6534-3.79940.27161460.242659156061100
3.7994-3.9720.28141380.233159546092100
3.972-4.18090.23751180.218959616079100
4.1809-4.4420.25051440.206559246068100
4.442-4.78370.21121440.191559506094100
4.7837-5.26280.22471610.188759556116100
5.2628-6.01890.2361570.21659956152100
6.0189-7.56290.26681630.233960196182100
7.5629-29.92490.22231760.22796115629199

+
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