[English] 日本語
Yorodumi
- PDB-5xhv: Crystal Structure Of Fab S40 In Complex With Influenza Hemaggluti... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5xhv
TitleCrystal Structure Of Fab S40 In Complex With Influenza Hemagglutinin, HA1 subunit.
Components
  • Hemagglutinin
  • S40 heavy chain
  • S40 light chain
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / VIRAL PROTEIN-IMMUNE SYSTEM / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


viral budding from plasma membrane / 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 / virion membrane
Similarity search - Function
Hemagglutinin; Chain A, domain 2 / Hemagglutinin Chain A, Domain 2 / 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 ...Hemagglutinin; Chain A, domain 2 / Hemagglutinin Chain A, Domain 2 / 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
Biological speciesInfluenza A virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.35 Å
AuthorsLee, C.C. / Wang, A.H.J. / Yu, C.M. / Yang, A.S.
CitationJournal: Sci Rep / Year: 2017
Title: High throughput discovery of influenza virus neutralizing antibodies from phage-displayed synthetic antibody libraries.
Authors: Chen, I.C. / Chiu, Y.K. / Yu, C.M. / Lee, C.C. / Tung, C.P. / Tsou, Y.L. / Huang, Y.J. / Lin, C.L. / Chen, H.S. / Wang, A.H. / Yang, A.S.
History
DepositionApr 24, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 15, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Hemagglutinin
E: Hemagglutinin
H: S40 heavy chain
L: S40 light chain
P: S40 heavy chain
Q: S40 light chain


Theoretical massNumber of molelcules
Total (without water)168,1006
Polymers168,1006
Non-polymers00
Water0
1
A: Hemagglutinin
P: S40 heavy chain
Q: S40 light chain


Theoretical massNumber of molelcules
Total (without water)84,0503
Polymers84,0503
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: Hemagglutinin
H: S40 heavy chain
L: S40 light chain


Theoretical massNumber of molelcules
Total (without water)84,0503
Polymers84,0503
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)200.395, 133.640, 133.136
Angle α, β, γ (deg.)90.00, 110.47, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Hemagglutinin /


Mass: 35986.641 Da / Num. of mol.: 2 / Fragment: HA1 subunit (UNP RESIDUES 18-341)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/California/07/2009(H1N1))
Strain: A/California/07/2009(H1N1) / Gene: HA
Production host: Insect cell expression vector pTIE1 (others)
References: UniProt: C3W5X2
#2: Antibody S40 heavy chain


Mass: 24445.262 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK-293 / Production host: Homo sapiens (human)
#3: Antibody S40 light chain


Mass: 23618.182 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK-293 / Production host: Homo sapiens (human)

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.97 Å3/Da / Density % sol: 75.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 8%(w/v) PEG 6000, 1N NaOH, 15% MPD, 0.1 M Na HEPES pH 7.5

-
Data collection

DiffractionMean temperature: 94 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Apr 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 3.35→25 Å / Num. obs: 34636 / % possible obs: 99.6 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.096 / Net I/σ(I): 17.3
Reflection shellResolution: 3.35→3.47 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.645 / Mean I/σ(I) obs: 2.4 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data processing
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3W9D, 3HC4, 3GBN

3w9d

3hc4

3gbn


Resolution: 3.35→25 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.899 / SU B: 26.695 / SU ML: 0.429 / Cross valid method: THROUGHOUT / ESU R Free: 0.58 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27452 1826 5 %RANDOM
Rwork0.22987 ---
obs0.23227 34487 76.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 173.528 Å2
Baniso -1Baniso -2Baniso -3
1--5.81 Å2-0 Å2-3.04 Å2
2--22.97 Å2-0 Å2
3----11.64 Å2
Refinement stepCycle: 1 / Resolution: 3.35→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11100 0 0 0 11100
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01911406
X-RAY DIFFRACTIONr_bond_other_d0.0020.0210450
X-RAY DIFFRACTIONr_angle_refined_deg1.4941.94815518
X-RAY DIFFRACTIONr_angle_other_deg0.977324196
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.56151434
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.41424.249466
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.072151822
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.691542
X-RAY DIFFRACTIONr_chiral_restr0.0790.21690
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02112952
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022606
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it11.60217.5645754
X-RAY DIFFRACTIONr_mcbond_other11.57717.5645753
X-RAY DIFFRACTIONr_mcangle_it17.94926.3157182
X-RAY DIFFRACTIONr_mcangle_other17.95326.3167183
X-RAY DIFFRACTIONr_scbond_it10.67817.525652
X-RAY DIFFRACTIONr_scbond_other10.67817.525652
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other16.97626.1318337
X-RAY DIFFRACTIONr_long_range_B_refined23.72212271
X-RAY DIFFRACTIONr_long_range_B_other23.72212272
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.35→3.435 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.38 65 -
Rwork0.258 1283 -
obs--39.29 %

+
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