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- PDB-7zfm: Engineered Protein Targeting the Zika Viral Envelope Fusion Loop -

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Basic information

Entry
Database: PDB / ID: 7zfm
TitleEngineered Protein Targeting the Zika Viral Envelope Fusion Loop
ComponentsPeptidyl-prolyl cis-trans isomerase A
KeywordsANTIVIRAL PROTEIN / ZIKV / Neutralization / E protein / Fusion Loop
Function / homology
Function and homology information


peptidyl-prolyl cis-trans isomerase activity / RNA polymerase II CTD heptapeptide repeat P3 isomerase activity / RNA polymerase II CTD heptapeptide repeat P6 isomerase activity / peptidylprolyl isomerase / protein folding / outer membrane-bounded periplasmic space / periplasmic space
Similarity search - Function
Cyclophilin-type peptidyl-prolyl cis-trans isomerase, E. coli cyclophilin A-like / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, conserved site / Cyclophilin-type peptidyl-prolyl cis-trans isomerase signature. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain profile. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain / Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD / Cyclophilin-like domain superfamily
Similarity search - Domain/homology
ACETIC ACID / TRIETHYLENE GLYCOL / SUCCINIC ACID / Peptidyl-prolyl cis-trans isomerase A
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.711 Å
AuthorsAthayde, D. / Archer, M. / Viana, I.F.T. / Adan, W.C.S. / Xavier, L.S.S. / Lins, R.D.
Funding support Portugal, 1items
OrganizationGrant numberCountry
Fundacao para a Ciencia e a Tecnologia Portugal
Citation
Journal: SSRN / Year: 2022
Title: In Vitro Neutralisation of Zika Virus by an Engineered Protein Targeting the Viral Envelope Fusion Loop
Authors: Viana, I.F.T. / Cruz, C.H.B. / Athayde, D. / Adan, W.C.S. / Xavier, L.S.S. / Archer, M. / Lins, R.D.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2012
Title: Towards automated crystallographic structure refinement with phenix.refine.
Authors: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D.
#2: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
#3: Journal: Acta Crystallogr.,Sect.D / Year: 2011
Title: Data processing and analysis with the autoPROC toolbox.
Authors: Vonrhein, C. / Flensburg, C. / Keller, P. / Sharff, A. / Smart, O. / Paciorek, W. / Womack, T. / Bricogne, G.
#4: Journal: Acta Crystallogr.,Sect.D / Year: 2010
Title: XDS.
Authors: Kabsch, W.
#5: Journal: Acta Crystallogr.,Sect.D / Year: 2006
Title: Scaling and assessment of data quality.
Authors: Evans, P.
#6: Journal: Acta Crystallogr.,Sect.D / Year: 2013
Title: How good are my data and what is the resolution?
Authors: Evans, P.R. / Murshudov, G.N.
#7: Journal: Acta Crystallogr.,Sect.D / Year: 2011
Title: Overview of the CCP4 suite and current developments.
Authors: Winn, M.D. / Ballard, C.C. / Cowtan, K.D. / Dodson, E.J. / Emsley, P. / Evans, P.R. / Keegan, R.M. / Krissinel, E.B. / Leslie, A.G. / McCoy, A. / McNicholas, S.J. / Murshudov, G.N. / Pannu, ...Authors: Winn, M.D. / Ballard, C.C. / Cowtan, K.D. / Dodson, E.J. / Emsley, P. / Evans, P.R. / Keegan, R.M. / Krissinel, E.B. / Leslie, A.G. / McCoy, A. / McNicholas, S.J. / Murshudov, G.N. / Pannu, N.S. / Potterton, E.A. / Powell, H.R. / Read, R.J. / Vagin, A. / Wilson, K.S.
History
DepositionApr 1, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 17, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / pdbx_initial_refinement_model
Item: _citation.country / _citation.journal_id_ISSN

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Peptidyl-prolyl cis-trans isomerase A
B: Peptidyl-prolyl cis-trans isomerase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,40427
Polymers41,3502
Non-polymers2,05425
Water5,242291
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A: Peptidyl-prolyl cis-trans isomerase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,96416
Polymers20,6751
Non-polymers1,28915
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Peptidyl-prolyl cis-trans isomerase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,44011
Polymers20,6751
Non-polymers76510
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.618, 81.618, 113.282
Angle α, β, γ (deg.)90, 90, 90
Int Tables number96
Space group name H-MP43212
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-1275-

HOH

21B-1213-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Peptidyl-prolyl cis-trans isomerase A / PPIase A / Cyclophilin A / Rotamase A / ZVAP3


Mass: 20675.021 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: ppiA, rot, rotA, b3363, JW3326 / Plasmid: pET14b / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Star pLysS / References: UniProt: P0AFL3, peptidylprolyl isomerase

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Non-polymers , 6 types, 316 molecules

#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: C2H6O2
#3: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C6H14O4
#5: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H4O2
#6: Chemical ChemComp-SIN / SUCCINIC ACID


Mass: 118.088 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 291 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.63 Å3/Da / Density % sol: 53.25 % / Description: Clear Octahedron Shaped Crystals
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1.0 M Succinic acid, 0.1 M Hepes pH 7.0 and 1% w/v PEG 2000 MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 29, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 1.711→66.221 Å / Num. obs: 37153 / % possible obs: 95.2 % / Redundancy: 12.91 %
Details: Some remarks regarding the mmCIF items written, the PDB Exchange Dictionary (PDBx/mmCIF) Version 5.0 supporting the data files in the current PDB archive (dictionary version 5.325, last ...Details: Some remarks regarding the mmCIF items written, the PDB Exchange Dictionary (PDBx/mmCIF) Version 5.0 supporting the data files in the current PDB archive (dictionary version 5.325, last updated 2020-04-13: http://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Index/) and the actual quantities provided by MRFANA (https://github.com/githubgphl/MRFANA) from the autoPROC package (https://www.globalphasing.com/autoproc/). In general, the mmCIF categories here should provide items that are currently used in the PDB archive. If there are alternatives, the one recommended by the PDB developers has been selected. The distinction between *_all and *_obs quantities is not always clear: often only one version is actively used within the PDB archive (or is the one recommended by PDB developers). The intention of distinguishing between classes of reflections before and after some kind of observation criterion was applied, can in principle be useful - but such criteria change in various ways through the data processing procedure (rejection of overloaded or too partial reflections, outlier/misfit rejection during scaling etc) and there is no retrospect computation of data scaling/merging statistics for the reflections used in the final refinement (where another observation criterion might have been applied). Typical data processing will usually only provide one version of statistics at various stages and these are given in the recommended item here, irrespective of the "_all" and "_obs" connotation, see e.g. the use of _reflns.pdbx_Rmerge_I_obs, _reflns.pdbx_Rrim_I_all and _reflns.pdbx_Rpim_I_all. Please note that all statistics related to "merged intensities" (or "merging") are based on inverse-variance weighting of the individual measurements making up a symmetry-unique reflection. This is standard for several decades now, even if some of the dictionary definitions seem to suggest that a simple "mean" or "average" intensity is being used instead. R-values are always given for all symmetry-equivalent reflections following Friedel's law, i.e. Bijvoet pairs are not treated separately (since we want to describe the overall mean intensity and not the mean I(+) and I(-) here). The Rrim metric is identical to the Rmeas R-value and only differs in name. _reflns.pdbx_number_measured_all is the number of measured intensities just before the final merging step (at which point no additional rejection takes place). _reflns.number_obs is the number of symmetry-unique observations, i.e. the result of merging those measurements via inverse-variance weighting. _reflns.pdbx_netI_over_sigmaI is based on the merged intensities (_reflns.number_obs) as expected. _reflns.pdbx_redundancy is synonymous with "multiplicity". The per-shell item _reflns_shell.number_measured_all corresponds to the overall value _reflns.pdbx_number_measured_all. The per-shell item _reflns_shell.number_unique_all corresponds to the overall value _reflns.number_obs. The per-shell item _reflns_shell.percent_possible_all corresponds to the overall value _reflns.percent_possible_obs. The per-shell item _reflns_shell.meanI_over_sigI_obs corresponds to the overall value given as _reflns.pdbx_netI_over_sigmaI. But be aware of the incorrect definition of the former in the current dictionary!
CC1/2: 1 / Rmerge(I) obs: 0.0451 / Rpim(I) all: 0.0127 / Rrim(I) all: 0.0469 / Net I/σ(I): 28.45 / Num. measured all: 479564
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. measured obsNum. unique allNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
5.011-66.22112.420.023685.3923061230611857185710.00690.024699.9
3.937-5.01113.660.024687.3125395253951859185910.00680.025699.9
3.417-3.93713.40.029275.3624879248791856185610.00810.0304100
3.095-3.41714.30.036862.8426579265791859185910.010.0382100
2.867-3.09514.520.047350.6626969269691857185710.01270.049100
2.692-2.86714.580.062239.612708927089185818580.9990.01680.0645100
2.553-2.69214.210.080731.412639726397185718570.9990.0220.0837100
2.439-2.55314.940.100925.932772227722185618560.9980.02690.1044100
2.342-2.43914.780.115922.962747227472185918590.9980.0310.12100
2.259-2.34214.60.137919.62714427144185918590.9970.03720.1429100
2.187-2.25914.120.189915.522617826178185418540.9950.05230.1971100
2.123-2.18714.730.217813.12740327403186018600.9940.05840.2256100
2.066-2.12314.80.275910.982747427474185618560.9910.07410.2858100
2.015-2.06614.840.34958.692760327603186018600.9860.09350.362100
1.967-2.01513.360.42766.342481924819185818580.9730.12090.4447100
1.924-1.96712.080.5384.662239222392185418540.9450.160.5618100
1.885-1.9249.730.75062.991811318113186118610.8660.24910.7927100
1.849-1.8858.290.78312.321539315393185618560.8070.28190.835399.6
1.804-1.8497.170.83561.851332013320185818580.6940.32460.901581.9
1.711-1.8047.621.09551.471416214162185918590.5780.41441.17654.9

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Processing

Software
NameVersionClassification
BUSTER2.10.4refinement
autoPROC1.0.5data reduction
Aimless0.7.4data scaling
XDSBUILT 20200417data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1J2A

1j2a


Resolution: 1.711→66.22 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.949 / SU R Cruickshank DPI: 0.152 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.126 / SU Rfree Blow DPI: 0.117 / SU Rfree Cruickshank DPI: 0.112
RfactorNum. reflection% reflectionSelection details
Rfree0.2206 1777 -RANDOM
Rwork0.1885 ---
obs0.19 37153 88.5 %-
Displacement parametersBiso mean: 40.54 Å2
Baniso -1Baniso -2Baniso -3
1--0.3939 Å20 Å20 Å2
2---0.3939 Å20 Å2
3---0.7878 Å2
Refine analyzeLuzzati coordinate error obs: 0.23 Å
Refinement stepCycle: LAST / Resolution: 1.711→66.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2520 0 135 291 2946
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0085321HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.059504HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1610SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes898HARMONIC5
X-RAY DIFFRACTIONt_it2797HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion352SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies15HARMONIC1
X-RAY DIFFRACTIONt_ideal_dist_contact4468SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.79
X-RAY DIFFRACTIONt_other_torsion15.15
LS refinement shellResolution: 1.711→1.76 Å
RfactorNum. reflection% reflection
Rfree0.3234 43 -
Rwork0.2879 --
obs--21.91 %
Refinement TLS params.

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)
10.63910.1554-0.42111.9148-0.19991.54080.00990.1671-0.05370.16710.0273-0.0558-0.0537-0.0558-0.0372-0.00380.0290.0281-0.06940.00130.006121.127245.246349.0288
21.49090.0693-0.29862.0964-1.13321.89280.09260.0632-0.10250.0632-0.31430.302-0.10250.3020.2217-0.1077-0.0584-0.0130.0760.079-0.056150.380850.311738.2431
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A3 - 167
2X-RAY DIFFRACTION1{ A|* }A1001 - 1204
3X-RAY DIFFRACTION2{ B|* }B3 - 167
4X-RAY DIFFRACTION2{ B|* }B1001 - 1202

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