[English] 日本語
Yorodumi
- PDB-6lxj: Crystal structure of human Z2B3 Fab in complex with influenza vir... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6lxj
TitleCrystal structure of human Z2B3 Fab in complex with influenza virus neuraminidase from A/Anhui/1/2013 (H7N9)
Components
  • Heavy chain of Z2B3 Fab
  • Light chain of Z2B3 Fab
  • Neuraminidase
KeywordsHYDROLASE/IMMUNE SYSTEM / antibody / antigen / complex / IMMUNE SYSTEM / HYDROLASE-IMMUNE SYSTEM complex
Function / homology
Function and homology information


: / : / : / exo-alpha-sialidase / viral budding from plasma membrane / carbohydrate metabolic process / host cell plasma membrane / virion membrane / metal ion binding / membrane
Similarity search - Function
Sialidase, Influenza viruses A/B / Glycoside hydrolase, family 34 / Neuraminidase / Sialidase superfamily / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesInfluenza A virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.903 Å
AuthorsJiang, H. / Peng, W. / Qi, J. / Chai, Y. / Song, H. / Shi, Y. / Gao, G.F. / Wu, Y.
Funding support China, 5items
OrganizationGrant numberCountry
Chinese Academy of SciencesXDB29010202 China
Ministry of Science and Technology (China)2018ZX10733403 China
Chinese Academy of SciencesXDB37030204 China
Ministry of Science and Technology (China)2018ZX10101004-001 China
Chinese Academy of Sciences2016086 China
CitationJournal: Mbio / Year: 2020
Title: Structure-Based Modification of an Anti-neuraminidase Human Antibody Restores Protection Efficacy against the Drifted Influenza Virus.
Authors: Jiang, H. / Peng, W. / Qi, J. / Chai, Y. / Song, H. / Bi, Y. / Rijal, P. / Wang, H. / Oladejo, B.O. / Liu, J. / Shi, Y. / Gao, G.F. / Townsend, A.R. / Wu, Y.
History
DepositionFeb 11, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 2, 2020Provider: repository / Type: Initial release
Revision 2.0Dec 9, 2020Group: Atomic model / Data collection / Derived calculations
Category: atom_site / pdbx_nonpoly_scheme ...atom_site / pdbx_nonpoly_scheme / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / struct_conn
Item: _atom_site.auth_seq_id / _pdbx_nonpoly_scheme.pdb_seq_num ..._atom_site.auth_seq_id / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _struct_conn.ptnr2_auth_seq_id
Revision 2.1Nov 29, 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
Revision 2.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Neuraminidase
B: Neuraminidase
C: Neuraminidase
D: Neuraminidase
H: Heavy chain of Z2B3 Fab
L: Light chain of Z2B3 Fab
E: Heavy chain of Z2B3 Fab
F: Light chain of Z2B3 Fab
J: Heavy chain of Z2B3 Fab
K: Light chain of Z2B3 Fab
M: Heavy chain of Z2B3 Fab
N: Light chain of Z2B3 Fab
hetero molecules


Theoretical massNumber of molelcules
Total (without water)376,37028
Polymers365,93112
Non-polymers10,44016
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area49820 Å2
ΔGint44 kcal/mol
Surface area118240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)201.307, 207.514, 207.702
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number21
Space group name H-MC222

-
Components

-
Antibody , 2 types, 8 molecules HEJMLFKN

#2: Antibody
Heavy chain of Z2B3 Fab


Mass: 25133.088 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm)
#3: Antibody
Light chain of Z2B3 Fab


Mass: 22796.049 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm)

-
Protein / Non-polymers , 2 types, 8 molecules ABCD

#1: Protein
Neuraminidase


Mass: 43553.516 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/Anhui/1-BALF_RG44/2013(H7N9))
Strain: A/Anhui/1-BALF_RG44/2013(H7N9) / Gene: NA / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A024E1X5, exo-alpha-sialidase
#8: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION

-
Sugars , 4 types, 12 molecules

#4: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#5: Polysaccharide
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1559.386 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-2DManpa1-3[DManpa1-3[DManpa1-6]DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,9,8/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-g1_d2-e1_e2-f1_g3-h1_g6-i1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#6: Polysaccharide alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c6-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-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.: 4
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
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 ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.96 Å3/Da / Density % sol: 58.5 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1M HEPES pH 7.5, 12% PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9793 Å
DetectorType: Nonius Kappa CCD / Detector: CCD / Date: May 11, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 94896 / % possible obs: 99.4 % / Redundancy: 6.7 % / CC1/2: 0.998 / Net I/σ(I): 16.7
Reflection shellResolution: 2.9→3 Å / Redundancy: 6.7 % / Num. unique obs: 94896 / CC1/2: 0.998 / % possible all: 99.4

-
Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MWJ, 5W0D

4mwj

5w0d


Resolution: 2.903→48.911 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.58
RfactorNum. reflection% reflection
Rfree0.2412 4742 5 %
Rwork0.1932 --
obs0.1956 94896 99.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 130.25 Å2 / Biso mean: 39.882 Å2 / Biso min: 10.29 Å2
Refinement stepCycle: final / Resolution: 2.903→48.911 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24832 0 691 0 25523
Biso mean--48.38 --
Num. residues----3238
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01226251
X-RAY DIFFRACTIONf_angle_d1.22335888
X-RAY DIFFRACTIONf_dihedral_angle_d15.3569738
X-RAY DIFFRACTIONf_chiral_restr0.074089
X-RAY DIFFRACTIONf_plane_restr0.0094493
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9034-2.93640.371510.28612845X-RAY DIFFRACTION95
2.9364-2.9710.35691350.27712930X-RAY DIFFRACTION97
2.971-3.00720.34841540.26492933X-RAY DIFFRACTION98
3.0072-3.04520.29591240.26272998X-RAY DIFFRACTION98
3.0452-3.08530.35451600.25822934X-RAY DIFFRACTION98
3.0853-3.12760.30851620.24982966X-RAY DIFFRACTION99
3.1276-3.17220.32351820.24712926X-RAY DIFFRACTION99
3.1722-3.21960.33921670.24662982X-RAY DIFFRACTION99
3.2196-3.26990.29211700.24372977X-RAY DIFFRACTION99
3.2699-3.32350.29521560.24142955X-RAY DIFFRACTION99
3.3235-3.38080.32021730.23792976X-RAY DIFFRACTION99
3.3808-3.44220.2681840.23062950X-RAY DIFFRACTION99
3.4422-3.50840.25061830.20662966X-RAY DIFFRACTION99
3.5084-3.580.23811610.2042968X-RAY DIFFRACTION99
3.58-3.65780.24141430.20573007X-RAY DIFFRACTION99
3.6578-3.74290.23751520.18593005X-RAY DIFFRACTION100
3.7429-3.83650.25371570.19053023X-RAY DIFFRACTION100
3.8365-3.94010.26911380.19513024X-RAY DIFFRACTION100
3.9401-4.0560.25331760.18172996X-RAY DIFFRACTION100
4.056-4.18690.21171500.16033073X-RAY DIFFRACTION100
4.1869-4.33640.18391470.15843016X-RAY DIFFRACTION100
4.3364-4.50990.1911490.1563080X-RAY DIFFRACTION100
4.5099-4.7150.17721520.14523014X-RAY DIFFRACTION100
4.715-4.96340.18861720.14963052X-RAY DIFFRACTION100
4.9634-5.2740.19361840.15973016X-RAY DIFFRACTION100
5.274-5.68070.23451570.16463045X-RAY DIFFRACTION100
5.6807-6.25130.20881430.18053112X-RAY DIFFRACTION100
6.2513-7.15350.22311270.18023105X-RAY DIFFRACTION100
7.1535-9.00340.2081570.17383123X-RAY DIFFRACTION100
9.0034-48.91830.22271760.19733157X-RAY DIFFRACTION98

+
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