[English] 日本語
Yorodumi
- PDB-6a0z: Crystal structure of broadly neutralizing antibody 13D4 bound to ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6a0z
TitleCrystal structure of broadly neutralizing antibody 13D4 bound to H5N1 influenza hemagglutinin, HA head region
Components
  • Antibody 13D4, Fab Heavy Chain
  • Antibody 13D4, Fab Light Chain
  • Hemagglutinin,Envelope glycoprotein
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / Immune complex / Antibody / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


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 / membrane
Similarity search - Function
Fibritin C-terminal / Fibritin C-terminal region / 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 ...Fibritin C-terminal / Fibritin C-terminal region / 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
Envelope glycoprotein / Hemagglutinin / Hemagglutinin
Similarity search - Component
Biological speciesInfluenza A virus
Human immunodeficiency virus 1
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.329 Å
AuthorsLi, S. / Li, T.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China31670934 China
National Natural Science Foundation of China30901077 China
CitationJournal: J. Virol. / Year: 2018
Title: Structural Basis for the Broad, Antibody-Mediated Neutralization of H5N1 Influenza Virus.
Authors: Lin, Q. / Li, T. / Chen, Y. / Lau, S.Y. / Wei, M. / Zhang, Y. / Zhang, Z. / Yao, Q. / Li, J. / Li, Z. / Wang, D. / Zheng, Q. / Yu, H. / Gu, Y. / Zhang, J. / Chen, H. / Li, S. / Xia, N.
History
DepositionJun 6, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 20, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 25, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Sep 19, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation_author.identifier_ORCID
Revision 2.0Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Polymer sequence / Structure summary
Category: chem_comp / entity ...chem_comp / entity / entity_poly / 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 / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 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 2.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Hemagglutinin,Envelope glycoprotein
H: Antibody 13D4, Fab Heavy Chain
L: Antibody 13D4, Fab Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,8735
Polymers110,4303
Non-polymers4422
Water5,386299
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5930 Å2
ΔGint-24 kcal/mol
Surface area31310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.245, 72.665, 76.704
Angle α, β, γ (deg.)90.00, 93.37, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Hemagglutinin,Envelope glycoprotein


Mass: 62911.617 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The fusion protein of Hemagglutinin (UNP RESIDUES 17-520, LINKER, Envelope glycoprotein (UNP RESIDUES 1-28), and HIS tags.
Source: (gene. exp.) Influenza A virus, (gene. exp.) Human immunodeficiency virus 1
Gene: HA / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: Q45ZR9, UniProt: M1E1E4, UniProt: Q6DQ34*PLUS
#2: Antibody Antibody 13D4, Fab Heavy Chain


Mass: 23888.648 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#3: Antibody Antibody 13D4, Fab Light Chain


Mass: 23630.027 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#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.: 299 / 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: 1.82 Å3/Da / Density % sol: 32.42 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M Bis-Tris-propane pH 6.5, 0.2 M NaAc and 18% (w/v) PEG 3350

-
Data collection

DiffractionMean temperature: 277.15 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97945 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 29, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 2.329→50 Å / Num. obs: 33998 / % possible obs: 99.8 % / Redundancy: 3.7 % / Rpim(I) all: 0.052 / Rsym value: 0.087 / Net I/σ(I): 19.2
Reflection shellResolution: 2.33→2.37 Å / Num. unique obs: 1670 / Rpim(I) all: 0.294 / Rsym value: 0.483

-
Processing

Software
NameVersionClassification
HKL-2000V706edata reduction
HKL-2000V706edata scaling
PHASERphasing
Cootmodel building
PHENIX1.10.1_2155refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2IBX, 6A0X

2ibx

6a0x


Resolution: 2.329→34.67 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.08
RfactorNum. reflection% reflection
Rfree0.2179 1591 4.68 %
Rwork0.1715 --
obs0.1736 33980 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.329→34.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5477 0 28 299 5804
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035652
X-RAY DIFFRACTIONf_angle_d0.5867702
X-RAY DIFFRACTIONf_dihedral_angle_d10.963346
X-RAY DIFFRACTIONf_chiral_restr0.045852
X-RAY DIFFRACTIONf_plane_restr0.003985
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.329-2.40420.29741440.21412872X-RAY DIFFRACTION98
2.4042-2.49010.26121320.20572945X-RAY DIFFRACTION100
2.4901-2.58970.261510.20562908X-RAY DIFFRACTION100
2.5897-2.70760.27171540.19842941X-RAY DIFFRACTION100
2.7076-2.85020.28121430.20142964X-RAY DIFFRACTION100
2.8502-3.02870.25931150.19722960X-RAY DIFFRACTION100
3.0287-3.26240.26751520.18752913X-RAY DIFFRACTION100
3.2624-3.59040.20041540.16692943X-RAY DIFFRACTION100
3.5904-4.10920.20241480.15222962X-RAY DIFFRACTION100
4.1092-5.17440.1641390.13282992X-RAY DIFFRACTION100
5.1744-34.67390.18491590.16812989X-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)
10.13690.25650.29990.58770.4470.6884-0.08520.15520.3808-0.0156-0.4248-0.3634-0.29160.2326-0.57920.52320.02780.19560.54480.31440.685156.037-3.1634-15.5358
20.24710.08560.39310.03290.11910.66850.0156-0.08290.3996-0.01110.2977-0.280.2923-0.05360.11620.36270.08140.15410.3688-0.00240.536341.7229-5.9087-6.8929
30.41540.40050.36110.53930.3150.59920.24580.13010.468-0.0829-0.1025-0.45-0.18990.05510.09130.35910.08390.16080.36470.14720.503247.1557-7.8325-8.3071
40.18610.1394-0.19260.88410.1210.03240.29660.3314-0.0074-0.5182-0.1324-0.3144-0.0341-0.03250.09390.5190.13610.04670.49030.06860.33839.9187-15.6731-12.2157
50.0663-0.0325-0.03020.0544-0.06870.24730.2554-0.16910.3719-0.2645-0.41080.0027-0.1053-0.0345-00.33860.0217-0.03760.3031-0.02190.387228.2797-5.24211.7476
60.8794-0.2694-0.11520.495-0.07930.27760.13730.0429-0.014-0.0751-0.1440.04140.07650.01-0.00640.30120.0305-0.03710.2079-0.0310.2132.38-18.41-3.755
70.12740.4021-0.00180.9082-0.00980.02070.12350.23710.25-0.5988-0.1961-0.25-0.12040.1369-0.06620.53860.10460.28320.54250.1250.563859.377-0.33-21.364
8-0.01530.0086-0.02090.03110.0420.0095-0.0356-0.0914-0.0486-0.34460.1090.38230.09360.17620.00210.30170.35460.42531.62820.33451.06868.234-11.2379-19.1291
90.8956-0.12840.02410.49850.19080.64170.0496-0.060.0624-0.0344-0.05930.1712-0.0578-0.0685-00.2078-0.0077-0.00510.2079-0.00130.234211.8317-3.909322.1391
10-0.03190.16530.2820.29870.57910.4129-0.0088-0.0777-0.0785-0.1199-0.09170.1541-0.1061-0.00420.00240.27-0.00150.03820.3009-0.00710.290313.34771.497130.0442
110.04090.069-0.09590.0013-0.05130.13070.0888-0.0114-0.0884-0.0166-0.24570.1053-0.246-0.27590.00360.30560.0416-0.03590.3623-0.03580.31099.592220.501157.6174
120.0592-0.038-0.01160.02280.00510.10220.10830.52710.13170.0826-0.06480.1748-0.14830.0117-0.00140.28710.01970.03290.4162-0.02820.30316.805515.340941.5188
130.367-0.2869-0.16990.24970.25230.62990.11240.12540.0093-0.0686-0.1572-0.2431-0.1178-0.093-0.00090.27110.0441-0.0010.3472-0.02020.37397.491718.74548.278
140.1972-0.14070.26480.2271-0.20540.23230.0055-0.1018-0.22040.23480.1294-0.3090.23550.0941-00.32570.0278-0.02310.3034-0.00770.289432.5191-9.400837.3219
150.1208-0.04810.1350.0644-0.09110.1682-0.03310.14170.60010.08670.0096-0.1572-0.0516-0.2459-0.00050.30880.0394-0.0010.2386-0.02970.290327.15740.854431.5551
160.24510.09880.3510.12430.32420.5448-0.00250.07670.0616-0.10810.0529-0.0983-0.0510.2632-0.00270.21490.0031-0.01280.2026-0.02560.253335.6017-1.711532.0715
170.0404-0.0707-0.05880.3776-0.0660.6916-0.0301-0.0833-0.00330.08930.09910.01730.10490.0094-00.1702-0.0008-0.01680.2384-0.02160.230917.87554.331447.0833
181.2309-0.52850.66820.4392-0.15320.8722-0.0838-0.3076-0.34450.11280.01340.0755-0.0021-0.0259-0.00030.2264-0.00340.02450.25950.01430.262511.95818.366462.1442
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 47 through 65 )
2X-RAY DIFFRACTION2chain 'A' and (resid 66 through 79 )
3X-RAY DIFFRACTION3chain 'A' and (resid 80 through 99 )
4X-RAY DIFFRACTION4chain 'A' and (resid 100 through 126 )
5X-RAY DIFFRACTION5chain 'A' and (resid 127 through 146 )
6X-RAY DIFFRACTION6chain 'A' and (resid 147 through 273 )
7X-RAY DIFFRACTION7chain 'A' and (resid 274 through 280 )
8X-RAY DIFFRACTION8chain 'A' and (resid 281 through 309 )
9X-RAY DIFFRACTION9chain 'H' and (resid 2 through 95 )
10X-RAY DIFFRACTION10chain 'H' and (resid 96 through 124 )
11X-RAY DIFFRACTION11chain 'H' and (resid 125 through 145 )
12X-RAY DIFFRACTION12chain 'H' and (resid 146 through 157 )
13X-RAY DIFFRACTION13chain 'H' and (resid 158 through 214 )
14X-RAY DIFFRACTION14chain 'L' and (resid 1 through 32 )
15X-RAY DIFFRACTION15chain 'L' and (resid 33 through 48 )
16X-RAY DIFFRACTION16chain 'L' and (resid 49 through 90 )
17X-RAY DIFFRACTION17chain 'L' and (resid 91 through 128 )
18X-RAY DIFFRACTION18chain 'L' and (resid 129 through 212 )

+
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