[English] 日本語
Yorodumi
- PDB-8eez: Crystal structure of a NHP anti-ZIKV neutralizing antibody rhMZ100-C -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8eez
TitleCrystal structure of a NHP anti-ZIKV neutralizing antibody rhMZ100-C
Components
  • rhMZ100-C antibody heavy chain
  • rhMZ100-C antibody light chain
KeywordsIMMUNE SYSTEM / ZIKV / ZIKV-specific / cross-protomer epitopes / VIRAL PROTEIN
Biological speciesMacaca mulatta (Rhesus monkey)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsSankhala, R.S. / Joyce, M.G.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Defense (DOD, United States)W81XWH-07-2-0067 United States
CitationJournal: Cell Rep / Year: 2023
Title: Zika-specific neutralizing antibodies targeting inter-dimer envelope epitopes.
Authors: Sankhala, R.S. / Dussupt, V. / Donofrio, G. / Gromowski, G.D. / De La Barrera, R.A. / Larocca, R.A. / Mendez-Rivera, L. / Lee, A. / Choe, M. / Zaky, W. / Mantus, G. / Jensen, J.L. / Chen, W. ...Authors: Sankhala, R.S. / Dussupt, V. / Donofrio, G. / Gromowski, G.D. / De La Barrera, R.A. / Larocca, R.A. / Mendez-Rivera, L. / Lee, A. / Choe, M. / Zaky, W. / Mantus, G. / Jensen, J.L. / Chen, W.H. / Gohain, N. / Bai, H. / McCracken, M.K. / Mason, R.D. / Leggat, D. / Slike, B.M. / Tran, U. / Jian, N. / Abbink, P. / Peterson, R. / Mendes, E.A. / Freitas de Oliveira Franca, R. / Calvet, G.A. / Bispo de Filippis, A.M. / McDermott, A. / Roederer, M. / Hernandez, M. / Albertus, A. / Davidson, E. / Doranz, B.J. / Rolland, M. / Robb, M.L. / Lynch, R.M. / Barouch, D.H. / Jarman, R.G. / Thomas, S.J. / Modjarrad, K. / Michael, N.L. / Krebs, S.J. / Joyce, M.G.
History
DepositionSep 7, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 30, 2023Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
H: rhMZ100-C antibody heavy chain
L: rhMZ100-C antibody light chain


Theoretical massNumber of molelcules
Total (without water)46,7322
Polymers46,7322
Non-polymers00
Water2,630146
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis, Reduced and native SDS PAGE
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3280 Å2
ΔGint-19 kcal/mol
Surface area19620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.981, 71.226, 114.176
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Antibody rhMZ100-C antibody heavy chain


Mass: 23274.891 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Production host: Homo sapiens (human)
#2: Antibody rhMZ100-C antibody light chain


Mass: 23456.941 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Production host: Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.44 Å3/Da / Density % sol: 49.5 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 22.5% PEG 4K, 22.5% IPA, 0.1M Na Citrate (pH5.6)

-
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 6M / Detector: PIXEL / Date: Aug 21, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.19→50 Å / Num. obs: 22274 / % possible obs: 92.5 % / Redundancy: 4.1 % / CC1/2: 0.99 / Net I/σ(I): 7.6
Reflection shellResolution: 2.19→2.26 Å / Num. unique obs: 1968 / CC1/2: 0.579

-
Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FQQ

4fqq


Resolution: 2.25→14.896 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2328 966 5 %
Rwork0.1855 18344 -
obs0.1879 19310 86.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 155.26 Å2 / Biso mean: 39.6002 Å2 / Biso min: 17.22 Å2
Refinement stepCycle: final / Resolution: 2.25→14.896 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3224 0 0 146 3370
Biso mean---40.31 -
Num. residues----434
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093301
X-RAY DIFFRACTIONf_angle_d1.1964501
X-RAY DIFFRACTIONf_chiral_restr0.064509
X-RAY DIFFRACTIONf_plane_restr0.009580
X-RAY DIFFRACTIONf_dihedral_angle_d7.9261966
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2502-2.36840.30241170.22782220233775
2.3684-2.51610.28131190.22732259237876
2.5161-2.70930.29111250.22832375250080
2.7093-2.980.25381440.20972747289191
2.98-3.40670.23751530.19252878303195
3.4067-4.27510.20071520.16132903305595
4.2751-14.89590.21321560.16582962311894
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)
10.0419-0.0337-0.00670.08060.0160.07160.00630.0835-0.09250.08670.01430.0848-0.11140.1281-00.14240.01820.0040.1444-0.01670.14922.547352.4524-9.1335
25.1076-1.2018-0.6391.2218-1.75763.9475-0.0088-0.45720.77460.74140.3453-0.4226-0.17690.1002-0.19340.3495-0.0578-0.00420.2399-0.01630.462-0.974455.125930.8515
33.6368-0.27650.09955.43233.0096.48950.1463-0.14170.24530.1516-0.2150.3451-0.1586-0.30080.04380.16070.0017-0.00470.18830.02370.2737-6.899751.239428.1303
4-0.00050.0056-0.0065-0.004-0.02270.0071-0.2283-0.10780.0858-0.02560.1157-0.1513-0.23910.1154-00.2137-0.0293-0.02040.26270.01530.24475.916576.6599-1.7775
5-0.00270.01060.00840.00480.01530.0087-0.11150.0629-0.0221-0.0167-0.03610.0384-0.04340.0343-00.1966-0.06290.00510.1635-0.03210.1521-2.101670.399-7.4875
60.005-0.0084-0.00330.0063-0.01280.01350.03420.0530.069-0.04170.1285-0.0247-0.1758-0.138800.2369-0.13460.05680.10240.1920.0233-0.267979.6007-9.3199
7-0.00210.0049-0.00260.00480.01760.011-0.00930.0293-0.0867-0.06450.2317-0.0302-0.0827-0.1874-00.2277-0.00260.03870.2364-0.06090.1354-3.456372.2297-2.3651
80.501-0.06150.27330.3471-0.42540.5044-0.2775-0.7112-0.02620.44340.0306-0.2737-0.2061-0.41620.14360.00480.01940.1092-0.175-0.05220.14880.233268.722711.8963
95.0523-1.29961.62753.0995-1.53584.84780.1391-0.2366-0.06330.0508-0.06440.0769-0.0458-0.0941-0.0840.3483-0.02780.01610.1208-0.06390.21174.54561.169724.461
102.0156-1.0412.21322.5132-1.06964.04510.17850.3030.0335-0.1714-0.06980.2139-0.2066-0.0689-0.06850.37880.03260.01650.2232-0.04610.32281.352364.262818.2546
115.7343-1.62831.97011.05230.42042.2380.0204-0.10760.05830.0294-0.0137-0.1055-0.1205-0.0011-0.01560.2969-0.07580.05250.17080.03290.23299.404464.296825.6462
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'H' and (resid 2 through 114 )H2 - 114
2X-RAY DIFFRACTION1chain 'H' and (resid 2 through 111 )H2 - 111
3X-RAY DIFFRACTION2chain 'H' and (resid 112 through 143 )H112 - 143
4X-RAY DIFFRACTION3chain 'H' and (resid 144 through 210 )H144 - 210
5X-RAY DIFFRACTION4chain 'L' and (resid 2 through 32 )L2 - 32
6X-RAY DIFFRACTION5chain 'L' and (resid 33 through 52 )L33 - 52
7X-RAY DIFFRACTION6chain 'L' and (resid 53 through 75 )L53 - 75
8X-RAY DIFFRACTION7chain 'L' and (resid 76 through 92 )L76 - 92
9X-RAY DIFFRACTION8chain 'L' and (resid 93 through 121 )L93 - 121
10X-RAY DIFFRACTION9chain 'L' and (resid 122 through 150 )L122 - 150
11X-RAY DIFFRACTION10chain 'L' and (resid 151 through 171 )L151 - 171
12X-RAY DIFFRACTION11chain 'L' and (resid 172 through 209 )L172 - 209

+
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://pdbjlvh1.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