[English] 日本語
Yorodumi
- PDB-5dur: Influenza A virus H5 hemagglutinin globular head in complex with ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5dur
TitleInfluenza A virus H5 hemagglutinin globular head in complex with antibody 100F4
Components
  • Heavy Chain of Antibody 100F4
  • Hemagglutinin
  • Light Chain of Antibody 100F4
KeywordsIMMUNE SYSTEM / Influenza virus / Antibody / Complex / Neutralize
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 (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 ...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 speciesHomo sapiens (human)
Influenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.82 Å
AuthorsZuo, T. / Sun, J. / Wang, G. / Zhou, P. / Wang, X. / Zhang, L.
CitationJournal: Nat Commun / Year: 2015
Title: Comprehensive analysis of antibody recognition in convalescent humans from highly pathogenic avian influenza H5N1 infection
Authors: Zuo, T. / Sun, J. / Wang, G. / Jiang, L. / Zuo, Y. / Li, D. / Shi, X. / Liu, X. / Fan, S. / Ren, H. / Hu, H. / Sun, L. / Zhou, B. / Liang, M. / Zhou, P. / Wang, X. / Zhang, L.
History
DepositionSep 20, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 16, 2015Provider: 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 / pdbx_struct_oper_list / 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 / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Oct 9, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
H: Heavy Chain of Antibody 100F4
L: Light Chain of Antibody 100F4
C: Hemagglutinin
B: Heavy Chain of Antibody 100F4
D: Light Chain of Antibody 100F4
A: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,1898
Polymers147,7476
Non-polymers4422
Water5,441302
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13820 Å2
ΔGint-63 kcal/mol
Surface area51590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.094, 101.223, 206.301
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Antibody Heavy Chain of Antibody 100F4


Mass: 24500.453 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK 293T / Production host: Homo sapiens (human)
#2: Antibody Light Chain of Antibody 100F4


Mass: 22837.170 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK 293T / Production host: Homo sapiens (human)
#3: Protein Hemagglutinin


Mass: 26535.771 Da / Num. of mol.: 2 / Fragment: globular head, UNP residues 61-284
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/Anhui/1/2005(H5N1))
Strain: A/Anhui/1/2005(H5N1) / Gene: HA / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q1WDM0
#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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 302 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.11 Å3/Da / Density % sol: 60.49 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 4.0M Potassium formate, Tris propane PH 9.0, 2% w/v PEGME 2000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 26, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.82→40.5 Å / Num. obs: 45011 / % possible obs: 99.8 % / Redundancy: 4.3 % / Net I/σ(I): 10.5

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 2.82→40.5 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2571 2259 5.02 %
Rwork0.2076 --
obs0.2101 45011 99.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.82→40.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9778 0 28 302 10108
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0110084
X-RAY DIFFRACTIONf_angle_d1.38513757
X-RAY DIFFRACTIONf_dihedral_angle_d15.1713593
X-RAY DIFFRACTIONf_chiral_restr0.0551554
X-RAY DIFFRACTIONf_plane_restr0.0071759
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8176-2.87890.31211240.26882357X-RAY DIFFRACTION89
2.8789-2.94580.28641340.26382688X-RAY DIFFRACTION100
2.9458-3.01950.28471450.26772617X-RAY DIFFRACTION100
3.0195-3.10110.31341330.24992657X-RAY DIFFRACTION100
3.1011-3.19230.30891420.24562688X-RAY DIFFRACTION100
3.1923-3.29530.28741450.22112636X-RAY DIFFRACTION100
3.2953-3.4130.27361420.22322648X-RAY DIFFRACTION100
3.413-3.54960.24741530.20842668X-RAY DIFFRACTION100
3.5496-3.7110.27841520.19842668X-RAY DIFFRACTION100
3.711-3.90660.25571390.19792691X-RAY DIFFRACTION100
3.9066-4.15110.21991380.17592674X-RAY DIFFRACTION100
4.1511-4.47120.20351560.15462695X-RAY DIFFRACTION100
4.4712-4.92050.17421250.152713X-RAY DIFFRACTION100
4.9205-5.63090.20691240.17312736X-RAY DIFFRACTION99
5.6309-7.08810.28091220.2272774X-RAY DIFFRACTION100
7.0881-40.51250.29321850.2462842X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.68840.4790.10522.42321.62672.007-0.0145-0.07130.062-0.1071-0.17360.3522-0.0816-0.3474-0.00140.22140.0166-0.02970.28910.0460.312589.9121350.0125646.5712
20.66650.81930.53591.88911.61813.28430.02030.0309-0.11920.20340.06540.07150.3413-0.11640.00490.20590.0203-0.0950.20260.02830.270999.9926335.8433653.6931
33.02621.5485-0.41272.6209-0.2641.9913-0.0749-0.0149-0.2280.01420.0096-0.29860.02660.1644-0.00030.3207-0.033-0.01530.2437-0.06020.230485.0336307.5348626.4528
43.12221.2084-0.18083.3439-0.1532.35980.0192-0.0329-0.3090.01760.0076-0.18750.16070.03620.00040.17420.0085-0.05450.2317-0.03610.1975151.9275377.5066661.1369
52.43950.81751.89911.41710.6272.56940.06890.31550.0996-0.08460.0445-0.0766-0.1490.28660.00420.22690.01660.06960.2342-0.04180.2066121.9683361.4187638.2739
62.25130.35761.12381.05590.41811.6834-0.0697-0.25380.2555-0.0617-0.08130.1558-0.2726-0.2198-0.00030.2490.03510.04650.2239-0.01220.2348107.6981369.8557647.2042
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain L
2X-RAY DIFFRACTION2chain H
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain A
5X-RAY DIFFRACTION5chain B
6X-RAY DIFFRACTION6chain D

+
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