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

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6mtx
TitleCrystal structure of a human anti-ZIKV-DENV neutralizing antibody MZ1 isolated following ZPIV vaccination
Components
  • MZ1 Heavy Chain
  • MZ1 Light Chain
KeywordsIMMUNE SYSTEM / Antibody / Vaccination
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.051 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
Department of Defense (DOD, United States)W81XWH-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
DepositionOct 22, 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 1.2Sep 22, 2021Group: Data collection / Database references / Category: database_2 / reflns_shell
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _reflns_shell.d_res_low
Revision 1.3Oct 11, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
H: MZ1 Heavy Chain
L: MZ1 Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,0934
Polymers46,9092
Non-polymers1842
Water5,206289
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Heavy and light chain of the Fab come together to form a heterodimer.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4140 Å2
ΔGint-21 kcal/mol
Surface area19280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.773, 66.806, 138.067
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Antibody MZ1 Heavy Chain


Mass: 23927.770 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 MZ1 Light Chain


Mass: 22981.408 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGLV1-44*01 / Details (production host): pVRC8400 / Cell line (production host): Expi293 / Production host: Homo sapiens (human)
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 289 / 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: 2.97 Å3/Da / Density % sol: 58.65 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.2 M ammonium sulfate, 0.1 M sodium acetate trihydrate (pH 4.6) and 25% (w/v) polyethylene glycol 4000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 35548 / % possible obs: 94.8 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.2 / Rpim(I) all: 0.08 / Rrim(I) all: 0.22 / Rsym value: 0.2 / Χ2: 0.93 / Net I/σ(I): 9
Reflection shellResolution: 2.05→2.12 Å / Num. unique obs: 3263 / Rpim(I) all: 0.54

-
Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4UTA

4uta


Resolution: 2.051→19.975 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2097 1544 5 %
Rwork0.1755 29325 -
obs0.1772 30869 87.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 151.63 Å2 / Biso mean: 36.3243 Å2 / Biso min: 11.89 Å2
Refinement stepCycle: final / Resolution: 2.051→19.975 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3236 0 28 289 3553
Biso mean--47 39.49 -
Num. residues----433
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073343
X-RAY DIFFRACTIONf_angle_d0.8894568
X-RAY DIFFRACTIONf_chiral_restr0.053522
X-RAY DIFFRACTIONf_plane_restr0.006582
X-RAY DIFFRACTIONf_dihedral_angle_d11.7621999
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Highest resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.051-2.11690.32273361120
2.1169-2.19250.264397183761
2.1925-2.28010.2369134256985
2.2801-2.38370.2292153289395
2.3837-2.50920.2419156298098
2.5092-2.66610.22391593011100
2.6661-2.87130.20241593033100
2.8713-3.15930.21991613049100
3.1593-3.61410.18821613053100
3.6141-4.54450.15421630.1467309399
4.54450.2393168319698
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)
13.9567-0.8392-1.91931.57390.16782.9009-0.1329-0.6148-0.14530.23220.0793-0.1140.17310.31540.01970.1689-0.0397-0.00610.23690.06430.1703-5.4177-15.972373.2483
24.28111.242-0.44283.2471-1.2321.2816-0.0529-0.0623-0.0206-0.23050.05430.10170.2626-0.08210.0850.08640.0292-0.00570.1830.04430.1821-13.1704-12.952767.7014
31.1620.2647-1.19531.21640.21181.6047-0.0143-0.2269-0.2430.1594-0.09120.04450.0177-0.07140.08760.1106-0.009-0.0160.23310.06890.1825-9.2203-18.608467.6487
43.5168-0.9892-0.81983.14161.31823.3466-0.0481-1.09890.4830.75610.05380.3398-0.090.22530.12640.3561-0.07250.03710.343-0.00570.4096-12.0863-3.343477.2396
51.6781-0.4107-0.07550.7502-0.21592.4720.1770.15070.1608-0.12730.097-0.0898-0.10.0398-0.20490.18690.00120.01840.1134-0.00490.20234.9666-12.293937.7087
62.37370.8555-1.89283.6572-0.85933.66870.2810.33370.1576-0.4971-0.11560.05230.1510.071-0.06820.18980.0520.01190.1592-0.03020.21678.0784-16.338228.6056
76.622-0.8554-0.51770.7144-0.42664.6948-0.0499-0.08820.22750.04850.15120.0859-0.216-0.18350.01610.3020.0092-0.00410.11090.02010.1467-5.82868.99858.828
81.75730.719-1.01731.9804-1.01882.30690.1026-0.29880.12440.3061-0.02670.083-0.40270.0596-0.06010.20510.00070.0240.2064-0.01430.1747-7.46264.812465.447
91.86890.93421.3063.66450.96542.9326-0.00020.0183-0.0014-0.0597-0.07420.05910.0282-0.07210.03910.133-0.00290.03660.10070.01790.1486-6.53-3.461139.3845
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'H' and (resid 1 through 39 )H1 - 39
2X-RAY DIFFRACTION2chain 'H' and (resid 40 through 59 )H40 - 59
3X-RAY DIFFRACTION3chain 'H' and (resid 60 through 95 )H60 - 95
4X-RAY DIFFRACTION4chain 'H' and (resid 96 through 106 )H96 - 106
5X-RAY DIFFRACTION5chain 'H' and (resid 107 through 188 )H107 - 188
6X-RAY DIFFRACTION6chain 'H' and (resid 189 through 214 )H189 - 214
7X-RAY DIFFRACTION7chain 'L' and (resid 1 through 24 )L1 - 24
8X-RAY DIFFRACTION8chain 'L' and (resid 25 through 114 )L25 - 114
9X-RAY DIFFRACTION9chain 'L' and (resid 115 through 210 )L115 - 210

+
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