[English] 日本語
Yorodumi
- PDB-5y2m: Crystal structure of a group 2 HA binding antibody AF4H1K1 Fab in... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5y2m
TitleCrystal structure of a group 2 HA binding antibody AF4H1K1 Fab in complex with the H4N6 duck isolate (H4-CZ/56) hemagglutinin
Components
  • (Hemagglutinin) x 2
  • a group 2 HA binding antibody AF4H1K1 Fab heavy chain
  • a group 2 HA binding antibody AF4H1K1 Fab light chain
KeywordsIMMUNE SYSTEM / neutralizing antibody / influenza virus / HA / H3-clade
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 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 / Immunoglobulins ...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 / Immunoglobulins / Alpha-Beta Complex / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesInfluenza A virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.8 Å
AuthorsXiao, H. / Qi, J. / Gao, F.G.
CitationJournal: To Be Published
Title: An H3-clade neutralizing antibody screened from an H7N9 patient that binds group 2 influenza A hemagglutinins
Authors: Xiao, H. / Qi, J. / Gao, F.G.
History
DepositionJul 26, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 13, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 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 1.2Nov 22, 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 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Hemagglutinin
D: Hemagglutinin
B: Hemagglutinin
E: Hemagglutinin
C: Hemagglutinin
F: Hemagglutinin
I: a group 2 HA binding antibody AF4H1K1 Fab heavy chain
J: a group 2 HA binding antibody AF4H1K1 Fab light chain
K: a group 2 HA binding antibody AF4H1K1 Fab heavy chain
L: a group 2 HA binding antibody AF4H1K1 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)268,69616
Polymers267,36810
Non-polymers1,3276
Water00
1
A: Hemagglutinin
D: Hemagglutinin
B: Hemagglutinin
E: Hemagglutinin
C: Hemagglutinin
F: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)170,25412
Polymers168,9276
Non-polymers1,3276
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area33460 Å2
ΔGint-128 kcal/mol
Surface area56330 Å2
MethodPISA
2
I: a group 2 HA binding antibody AF4H1K1 Fab heavy chain
J: a group 2 HA binding antibody AF4H1K1 Fab light chain


Theoretical massNumber of molelcules
Total (without water)49,2212
Polymers49,2212
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3510 Å2
ΔGint-24 kcal/mol
Surface area19930 Å2
MethodPISA
3
K: a group 2 HA binding antibody AF4H1K1 Fab heavy chain
L: a group 2 HA binding antibody AF4H1K1 Fab light chain


Theoretical massNumber of molelcules
Total (without water)49,2212
Polymers49,2212
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3590 Å2
ΔGint-24 kcal/mol
Surface area19860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.175, 140.940, 138.100
Angle α, β, γ (deg.)90.00, 95.31, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Hemagglutinin


Mass: 35966.461 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (strain A/Duck/Czechoslovakia/1956 H4N6)
Strain: A/Duck/Czechoslovakia/1956 H4N6 / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A3KF09
#2: Protein Hemagglutinin


Mass: 20342.391 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (strain A/Duck/Czechoslovakia/1956 H4N6)
Strain: A/Duck/Czechoslovakia/1956 H4N6 / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A3KF09
#3: Antibody a group 2 HA binding antibody AF4H1K1 Fab heavy chain


Mass: 24977.014 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#4: Antibody a group 2 HA binding antibody AF4H1K1 Fab light chain


Mass: 24243.838 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#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.: 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 protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.14 Å3/Da / Density % sol: 70.28 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M potassium sodium tartrate tetrahydrate, 0.1 M Bis-Tris pH6.5, 10% polyethylene glycol 10,000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.8→50 Å / Num. obs: 43204 / % possible obs: 99.8 % / Redundancy: 4 % / Net I/σ(I): 0.255
Reflection shellResolution: 3.8→3.94 Å / Mean I/σ(I) obs: 1.9 / Num. unique obs: 4301 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XL1

5xl1


Resolution: 3.8→49.212 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.86
RfactorNum. reflection% reflection
Rfree0.2774 2164 5.02 %
Rwork0.2355 --
obs0.2377 43072 99.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.8→49.212 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18231 0 84 0 18315
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00418741
X-RAY DIFFRACTIONf_angle_d0.75825412
X-RAY DIFFRACTIONf_dihedral_angle_d14.2826798
X-RAY DIFFRACTIONf_chiral_restr0.0342804
X-RAY DIFFRACTIONf_plane_restr0.0043336
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.7901-3.87820.33551280.31192605X-RAY DIFFRACTION95
3.8782-3.97520.40191360.35112733X-RAY DIFFRACTION99
3.9752-4.08260.31221550.27582718X-RAY DIFFRACTION100
4.0826-4.20270.30121390.26072726X-RAY DIFFRACTION100
4.2027-4.33820.27251280.23712757X-RAY DIFFRACTION100
4.3382-4.49320.28231770.2382690X-RAY DIFFRACTION100
4.4932-4.6730.25421600.22382708X-RAY DIFFRACTION100
4.673-4.88550.27841370.21742760X-RAY DIFFRACTION100
4.8855-5.14280.25111530.222736X-RAY DIFFRACTION100
5.1428-5.46460.2451470.21812744X-RAY DIFFRACTION100
5.4646-5.88590.28211390.23092744X-RAY DIFFRACTION100
5.8859-6.4770.28871470.22782757X-RAY DIFFRACTION100
6.477-7.41150.27181310.22062772X-RAY DIFFRACTION100
7.4115-9.32730.24641390.20272767X-RAY DIFFRACTION100
9.3273-49.21590.25261480.20932691X-RAY DIFFRACTION95
Refinement TLS params.Method: refined / Origin x: 15.7004 Å / Origin y: -23.8604 Å / Origin z: 13.7179 Å
111213212223313233
T0.3511 Å2-0.0206 Å20.01 Å2-0.3446 Å20.0075 Å2--0.3127 Å2
L0.1988 °20.026 °20.0204 °2-0.3763 °2-0.0145 °2---0.0195 °2
S0.0521 Å °0.0168 Å °0.0467 Å °0.1247 Å °-0.0992 Å °0.0071 Å °0.0619 Å °0.0625 Å °-0.0014 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://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