[English] 日本語
Yorodumi
- PDB-6nis: Crystal structure of a human anti-ZIKV-DENV neutralizing antibody... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6nis
TitleCrystal structure of a human anti-ZIKV-DENV neutralizing antibody MZ24 isolated following ZPIV vaccination
Components
  • MZ24 antibody heavy chain
  • MZ24 antibody light chain
KeywordsIMMUNE SYSTEM / ZIKV-DENV / Antibody / human / Vaccination / ANTIVIRAL PROTEIN
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.113 Å
AuthorsSankhala, R.S. / Dussupt, V. / Donofrio, G. / Choe, M. / Modjarrad, K. / Michael, N.L. / Krebs, S.J. / Joyce, M.G.
Funding support United States, 1items
OrganizationGrant numberCountry
Other governmentW81XWH-07-2-0067 United States
CitationJournal: Nat Med / Year: 2020
Title: Potent Zika and dengue cross-neutralizing antibodies induced by Zika vaccination in a dengue-experienced donor.
Authors: Dussupt, V. / Sankhala, R.S. / Gromowski, G.D. / Donofrio, G. / De La Barrera, R.A. / Larocca, R.A. / Zaky, W. / Mendez-Rivera, L. / Choe, M. / Davidson, E. / McCracken, M.K. / Brien, J.D. / ...Authors: Dussupt, V. / Sankhala, R.S. / Gromowski, G.D. / Donofrio, G. / De La Barrera, R.A. / Larocca, R.A. / Zaky, W. / Mendez-Rivera, L. / Choe, M. / Davidson, E. / McCracken, M.K. / Brien, J.D. / Abbink, P. / Bai, H. / Bryan, A.L. / Bias, C.H. / Berry, I.M. / Botero, N. / Cook, T. / Doria-Rose, N.A. / Escuer, A.G.I. / Frimpong, J.A. / Geretz, A. / Hernandez, M. / Hollidge, B.S. / Jian, N. / Kabra, K. / Leggat, D.J. / Liu, J. / Pinto, A.K. / Rutvisuttinunt, W. / Setliff, I. / Tran, U. / Townsley, S. / Doranz, B.J. / Rolland, M. / McDermott, A.B. / Georgiev, I.S. / Thomas, R. / Robb, M.L. / Eckels, K.H. / Barranco, E. / Koren, M. / Smith, D.R. / Jarman, R.G. / George, S.L. / Stephenson, K.E. / Barouch, D.H. / Modjarrad, K. / Michael, N.L. / Joyce, M.G. / Krebs, S.J.
History
DepositionDec 31, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 6, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Apr 7, 2021Group: Data collection / Category: reflns / Item: _reflns.pdbx_redundancy
Revision 1.3Oct 11, 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 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
H: MZ24 antibody heavy chain
L: MZ24 antibody light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,27312
Polymers46,8052
Non-polymers46810
Water6,431357
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Gel-filtration and native PAGE
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5410 Å2
ΔGint-102 kcal/mol
Surface area20130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.850, 66.667, 134.416
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Antibody MZ24 antibody heavy chain


Mass: 23876.615 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGHV4-59*08 / Details (production host): pVRC8400 / Cell line (production host): Expi293 / Production host: Homo sapiens (human)
#2: Antibody MZ24 antibody light chain


Mass: 22928.279 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGLV1-44*01 / Cell line (production host): Expi293 / Production host: Homo sapiens (human)
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 357 / 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: 3.06 Å3/Da / Density % sol: 59.75 % / Description: Rod shape
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 0.1 M Citric acid/NaOH (pH 4.0), 1M LiCl and 20% PEG 6,000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.97 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 12, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.11→28.8 Å / Num. obs: 35154 / % possible obs: 99.7 % / Rsym value: 0.1 / Net I/σ(I): 12.8
Reflection shellResolution: 2.11→2.12 Å / Num. unique obs: 5276 / Rsym value: 0.677

-
Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6MTX

6mtx


Resolution: 2.113→14.984 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2003 1668 4.99 %
Rwork0.1647 --
obs0.1665 33454 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.113→14.984 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3271 0 20 357 3648
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033375
X-RAY DIFFRACTIONf_angle_d0.7674613
X-RAY DIFFRACTIONf_dihedral_angle_d14.3932021
X-RAY DIFFRACTIONf_chiral_restr0.048529
X-RAY DIFFRACTIONf_plane_restr0.005587
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.113-2.1750.25621330.22122553X-RAY DIFFRACTION98
2.175-2.2450.24611360.20932615X-RAY DIFFRACTION100
2.245-2.3250.29951400.20322607X-RAY DIFFRACTION100
2.325-2.41770.23851340.20842604X-RAY DIFFRACTION100
2.4177-2.52720.26151410.20352639X-RAY DIFFRACTION100
2.5272-2.65980.22971390.19642643X-RAY DIFFRACTION100
2.6598-2.82540.2451370.18362627X-RAY DIFFRACTION100
2.8254-3.04190.19661390.17772662X-RAY DIFFRACTION100
3.0419-3.34490.19981360.16492652X-RAY DIFFRACTION100
3.3449-3.82190.18651440.14712659X-RAY DIFFRACTION100
3.8219-4.78890.16461440.12882712X-RAY DIFFRACTION100
4.7889-14.98430.16911450.1512813X-RAY DIFFRACTION100
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)
16.32620.7172-0.20283.2603-0.64494.7845-0.19450.19250.6199-0.34640.17820.444-0.1565-0.48990.02160.24250.0198-0.05090.25050.02350.364341.658524.816359.1475
20.4756-0.3527-0.23210.69290.41241.18610.0345-0.0027-0.0811-0.0921-0.0460.1165-0.0047-0.17310.01070.2708-0.0194-0.02290.2586-0.00090.312953.593115.630141.7808
32.3856-0.2123-1.67772.2182-0.41913.4384-0.32160.1157-0.2734-0.29980.1113-0.20470.57050.02840.16550.3223-0.01970.0930.2882-0.02410.299242.28412.627965.7689
42.5378-1.9464-4.21631.62133.01888.3453-0.1948-0.03730.0340.29770.05660.08250.5317-0.22450.1950.22-0.07150.02290.2753-0.03530.338252.6933.136758.3239
52.42510.4347-0.59337.4594-1.21843.88420.0563-0.09660.05910.308-0.0477-0.4879-0.04940.247-0.02260.22560.0002-0.02310.194-0.03930.261871.65274.704136.0753
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'H' and (resid 1 through 76 )
2X-RAY DIFFRACTION2chain 'H' and (resid 77 through 216 )
3X-RAY DIFFRACTION3chain 'L' and (resid 1 through 93 )
4X-RAY DIFFRACTION4chain 'L' and (resid 94 through 118 )
5X-RAY DIFFRACTION5chain 'L' and (resid 119 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