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- PDB-6u5e: RT XFEL structure of CypA solved using celloluse carrier media -

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Basic information

Entry
Database: PDB / ID: 6u5e
TitleRT XFEL structure of CypA solved using celloluse carrier media
ComponentsPeptidyl-prolyl cis-trans isomerase A
KeywordsISOMERASE / Peptidyl-prolyl / cis-trans / cyclophilin
Function / homology
Function and homology information


negative regulation of protein K48-linked ubiquitination / negative regulation of viral life cycle / regulation of apoptotic signaling pathway / cell adhesion molecule production / lipid droplet organization / heparan sulfate binding / regulation of viral genome replication / leukocyte chemotaxis / endothelial cell activation / virion binding ...negative regulation of protein K48-linked ubiquitination / negative regulation of viral life cycle / regulation of apoptotic signaling pathway / cell adhesion molecule production / lipid droplet organization / heparan sulfate binding / regulation of viral genome replication / leukocyte chemotaxis / endothelial cell activation / virion binding / Basigin interactions / negative regulation of stress-activated MAPK cascade / cyclosporin A binding / Minus-strand DNA synthesis / Plus-strand DNA synthesis / Uncoating of the HIV Virion / Early Phase of HIV Life Cycle / Integration of provirus / APOBEC3G mediated resistance to HIV-1 infection / Calcineurin activates NFAT / viral release from host cell / Binding and entry of HIV virion / positive regulation of viral genome replication / protein peptidyl-prolyl isomerization / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / positive regulation of protein dephosphorylation / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / activation of protein kinase B activity / neutrophil chemotaxis / negative regulation of protein phosphorylation / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / positive regulation of protein secretion / Assembly Of The HIV Virion / negative regulation of protein kinase activity / Budding and maturation of HIV virion / neuron differentiation / platelet activation / platelet aggregation / SARS-CoV-1 activates/modulates innate immune responses / unfolded protein binding / integrin binding / protein folding / Platelet degranulation / positive regulation of NF-kappaB transcription factor activity / cellular response to oxidative stress / secretory granule lumen / vesicle / ficolin-1-rich granule lumen / positive regulation of MAPK cascade / response to hypoxia / positive regulation of protein phosphorylation / focal adhesion / apoptotic process / Neutrophil degranulation / protein-containing complex / RNA binding / extracellular space / extracellular exosome / extracellular region / membrane / nucleus / cytoplasm / cytosol
Similarity search - Function
Cyclophilin-like / Cyclophilin / Cyclophilin-type peptidyl-prolyl cis-trans isomerase / 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 / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Peptidyl-prolyl cis-trans isomerase A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 1.56 Å
AuthorsWolff, A.M. / Nango, E. / Nakane, T. / Young, I.D. / Brewster, A.S. / Sugahara, M. / Tanaka, R. / Sauter, N.K. / Tono, K. / Iwata, S. ...Wolff, A.M. / Nango, E. / Nakane, T. / Young, I.D. / Brewster, A.S. / Sugahara, M. / Tanaka, R. / Sauter, N.K. / Tono, K. / Iwata, S. / Fraser, J.S. / Thompson, M.C.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM123159 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM124149 United States
National Science Foundation (NSF, United States)STC-1231306 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM117126 United States
CitationJournal: Iucrj / Year: 2020
Title: Comparing serial X-ray crystallography and microcrystal electron diffraction (MicroED) as methods for routine structure determination from small macromolecular crystals
Authors: Wolff, A.M. / Young, I.D. / Sierra, R.G. / Brewster, A.S. / Martynowycz, M.W. / Nango, E. / Sugahara, M. / Nakane, T. / Ito, K. / Aquila, A. / Bhowmick, A. / Biel, J.T. / Carbajo, S. / ...Authors: Wolff, A.M. / Young, I.D. / Sierra, R.G. / Brewster, A.S. / Martynowycz, M.W. / Nango, E. / Sugahara, M. / Nakane, T. / Ito, K. / Aquila, A. / Bhowmick, A. / Biel, J.T. / Carbajo, S. / Cohen, A.E. / Cortez, S. / Gonzalez, A. / Hino, T. / Im, D. / Koralek, J.D. / Kubo, M. / Lazarou, T.S. / Nomura, T. / Owada, S. / Samelson, A. / Tanaka, T. / Tanaka, R. / Thompson, E.M. / van den Bedem, H. / Woldeyes, R.A. / Yumoto, F. / Zhao, W. / Tono, K. / Boutet, S. / Iwata, S. / Gonen, T. / Sauter, N.K. / Fraser, J.S. / Thompson, M.C.
History
DepositionAug 27, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 29, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 12, 2020Group: Database references / Structure summary / Category: audit_author / citation_author
Revision 1.2Mar 11, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _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.title / _citation.year / _citation_author.name
Revision 1.3Aug 16, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_related_exp_data_set
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 11, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peptidyl-prolyl cis-trans isomerase A


Theoretical massNumber of molelcules
Total (without water)18,0371
Polymers18,0371
Non-polymers00
Water2,684149
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.000, 52.600, 89.200
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Peptidyl-prolyl cis-trans isomerase A / PPIase A / Cyclophilin A / Cyclosporin A-binding protein / Rotamase A


Mass: 18036.504 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPIA, CYPA / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P62937, peptidylprolyl isomerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / Source method: isolated from a natural source / Formula: H2O

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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: 2.8 Å3/Da / Density % sol: 56.02 %
Crystal growTemperature: 291 K / Method: batch mode / pH: 7.5 / Details: 100 mM HEPES, pH 7.5, 5 mM TCEP, 20% PEG3350

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Data collection

DiffractionMean temperature: 291 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SACLA / Beamline: BL3 / Wavelength: 1.24 Å
DetectorType: MPCCD / Detector: CCD / Date: Nov 29, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.24 Å / Relative weight: 1
ReflectionResolution: 1.56→20 Å / Num. obs: 29527 / % possible obs: 100 % / Redundancy: 261 % / Biso Wilson estimate: 24.82 Å2 / CC1/2: 0.993 / R split: 0.0794 / Net I/σ(I): 7.91
Reflection shellResolution: 1.56→1.58 Å / Redundancy: 40.5 % / Mean I/σ(I) obs: 1.46 / Num. unique obs: 1477 / CC1/2: 0.586 / R split: 0.66 / % possible all: 100
Serial crystallography measurementPulse duration: 10 fsec. / XFEL pulse repetition rate: 30 Hz
Serial crystallography sample deliveryDescription: Cellulose (Sugahara et al., 2017) / Method: injection
Serial crystallography data reductionFrames indexed: 23947

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
DIALSdata collection
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YUM

4yum


Resolution: 1.56→19.9 Å / SU ML: 0.1496 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 15.8797
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1509 929 3.15 %
Rwork0.1348 28598 -
obs0.1353 29527 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.62 Å2
Refinement stepCycle: LAST / Resolution: 1.56→19.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1249 0 0 149 1398
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01511446
X-RAY DIFFRACTIONf_angle_d1.29791959
X-RAY DIFFRACTIONf_chiral_restr0.0814198
X-RAY DIFFRACTIONf_plane_restr0.0093266
X-RAY DIFFRACTIONf_dihedral_angle_d16.5416867
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.56-1.640.28041320.23764027X-RAY DIFFRACTION99.98
1.64-1.750.17461280.15844021X-RAY DIFFRACTION100
1.75-1.880.15921310.13894036X-RAY DIFFRACTION100
1.88-2.070.13551330.11874057X-RAY DIFFRACTION100
2.07-2.370.14661330.12074053X-RAY DIFFRACTION100
2.37-2.980.15131330.13864111X-RAY DIFFRACTION100
2.98-19.90.14411390.13224293X-RAY DIFFRACTION99.98
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)
13.599767050270.706886395074-1.278756438241.83821879135-0.08512500262294.716119057650.0417877137352-0.216808069365-0.08545802305080.245670260069-0.0477019177242-0.07587537625480.1853894849970.2338433430050.01834718154240.2923488615730.00836811519762-0.006437686531350.213364554290.02966136214270.215606696954.433070567596.0056453296622.7491975782
23.42076336420.689668629331-1.054746082632.76459747633-0.9422751093973.54726536731-0.0227373541404-0.0504100154326-0.1871546355850.153213282991-0.0230368768774-0.1612376697830.1778542650880.2737995366860.05522254543440.1911024664920.0285896516351-0.01723981645180.1776180411560.01435073933060.1685877145639.291168052546.3833151396517.974753592
32.991747631960.9926538098150.8505026497342.659533719291.182607286744.04734131294-0.0200738348026-0.0165799360847-0.0367235959902-0.01719310903080.092005009605-0.00466369649638-0.214407675750.00135165500299-0.07107476623650.2257018558470.002136162635120.02228564658010.1664762192680.008385291205350.2007572553521.3487377282113.858627187815.4650867296
43.37248632073-1.03551823259-1.344917706530.9759011944430.4586031721262.0531659630.1725881343980.01588016054430.386963971422-0.0956114509937-0.026089473082-0.138508862642-0.4561913907420.178773749822-0.1433563160040.307109750824-0.03108234511770.02117373641670.208130344146-0.0113705622850.2737141147858.5773419008921.768836411312.8791568559
53.402538539351.63434287512-1.585846615982.60899354281-0.5933529145563.39659018769-0.1150555588420.0696865681699-0.300779968104-0.0841517363653-0.0199211770398-0.1086859164580.40626401610.1127749539560.1421771708520.241103962950.0409161105050.009774453992050.201220484116-0.007131189977380.2365307912148.820993891675.398099483195.23240691336
62.34594746860.174353863657-1.4378356160.65859782429-0.1731534085333.4758269050.06767036163250.1379861756910.037518034155-0.00756981328327-0.0300625409337-0.00969921684233-0.0259338425651-0.144650518602-0.03518603280720.1800449455760.0224337731840.002552940884360.1817676605330.006189019555150.1795732570684.1776289495511.22812486184.87957931412
73.654733270021.31987603154-3.047654819991.424948580120.0190856563984.51730186442-0.162291224072-0.0194263266446-0.1821659491420.00987742314262-0.023224398323-0.1904399451250.2342032908530.1010302488260.1371816432720.2037588840080.03618587355370.00108133950070.156821709036-0.002131442355360.2245749425846.932845875883.992815848978.66206689392
82.64091934057-3.769803340051.64912755475.77313532317-1.702560559072.114634268690.0907278762851-0.0360398671367-0.156402681702-0.3088585222730.1591878598670.3555981015910.243050661553-0.335362892313-0.2181211367380.304746652693-0.04748662970990.002771211297530.2682789463170.05571010450450.243225219051-7.358287720672.8079339227916.9436113583
93.877079085410.5525917841711.768078366431.031015262010.4981455370625.855625861590.0154300249697-0.3800319346530.04643477702920.1000708363150.01911130105610.156358637993-0.151331620509-0.682384995969-0.03268262154030.2829349514940.008730053966010.03443264925930.2019204914210.0121302788670.244357683605-4.9673770612.123664359818.4034079607
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 14 )
2X-RAY DIFFRACTION2chain 'A' and (resid 15 through 41 )
3X-RAY DIFFRACTION3chain 'A' and (resid 42 through 64 )
4X-RAY DIFFRACTION4chain 'A' and (resid 65 through 84 )
5X-RAY DIFFRACTION5chain 'A' and (resid 85 through 100 )
6X-RAY DIFFRACTION6chain 'A' and (resid 101 through 122 )
7X-RAY DIFFRACTION7chain 'A' and (resid 123 through 135 )
8X-RAY DIFFRACTION8chain 'A' and (resid 136 through 145 )
9X-RAY DIFFRACTION9chain 'A' and (resid 146 through 164 )

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