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- PDB-6u5d: RT XFEL structure of CypA solved using LCP injection system -

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Basic information

Entry
Database: PDB / ID: 6u5d
TitleRT XFEL structure of CypA solved using LCP injection system
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 / negative regulation of stress-activated MAPK cascade / endothelial cell activation ...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 / negative regulation of stress-activated MAPK cascade / endothelial cell activation / virion binding / Basigin interactions / 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 / positive regulation of viral genome replication / Binding and entry of HIV virion / 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 aggregation / platelet activation / SARS-CoV-1 activates/modulates innate immune responses / unfolded protein binding / integrin binding / protein folding / Platelet degranulation / cellular response to oxidative stress / positive regulation of NF-kappaB transcription factor activity / secretory granule lumen / vesicle / ficolin-1-rich granule lumen / positive regulation of MAPK cascade / positive regulation of protein phosphorylation / focal adhesion / apoptotic process / Neutrophil degranulation / protein-containing complex / extracellular space / RNA binding / extracellular exosome / extracellular region / membrane / nucleus / cytosol / cytoplasm
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: 1.65 Å
AuthorsWolff, A.M. / Young, I.D. / Sierra, R.G. / Brewster, A.S. / Koralek, J.D. / Boutet, S. / Sauter, N.K. / 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
Water2,846158
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 area7570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.010, 52.610, 89.320
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 / Water


Mass: 18.015 Da / Num. of mol.: 158 / 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: 56.09 %
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: SLAC LCLS / Beamline: MFX / Wavelength: 1.31 Å
DetectorType: RAYONIX MX170-HS / Detector: CCD / Date: Aug 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.31 Å / Relative weight: 1
ReflectionResolution: 1.65→20 Å / Num. obs: 25034 / % possible obs: 99.89 % / Redundancy: 98.9 % / Biso Wilson estimate: 19.85 Å2 / CC1/2: 0.945 / R split: 0.149 / Net I/σ(I): 4.062
Reflection shellResolution: 1.65→1.68 Å / Mean I/σ(I) obs: 1.076 / Num. unique obs: 1216 / CC1/2: 0.567 / R split: 0.543
Serial crystallography measurementPulse duration: 45 fsec. / XFEL pulse repetition rate: 10 Hz
Serial crystallography sample deliveryDescription: LCP (Weierstall et al., 2014) / Method: injection
Serial crystallography data reductionFrames indexed: 11821

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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: PDB entry 4YUM

4yum


Resolution: 1.65→17.43 Å / SU ML: 0.1519 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.1489
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1671 787 3.14 %
Rwork0.1434 24247 -
obs0.1442 25034 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.78 Å2
Refinement stepCycle: LAST / Resolution: 1.65→17.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1249 0 0 158 1407
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00351447
X-RAY DIFFRACTIONf_angle_d0.65661966
X-RAY DIFFRACTIONf_chiral_restr0.0515198
X-RAY DIFFRACTIONf_plane_restr0.0035269
X-RAY DIFFRACTIONf_dihedral_angle_d16.5258867
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.750.23671260.23163950X-RAY DIFFRACTION99.71
1.75-1.890.20151300.17323993X-RAY DIFFRACTION100
1.89-2.080.17671300.14913986X-RAY DIFFRACTION99.98
2.08-2.380.1611320.12864018X-RAY DIFFRACTION99.95
2.38-2.990.16961330.14614057X-RAY DIFFRACTION100
2.99-17.430.151360.12974243X-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)
13.4984376010.118519115167-0.9910459139882.02213454769-0.6044473927643.49676121643-0.0335617757077-0.109579323213-0.1964527040030.150164143178-0.0520654753461-0.08981661134980.2285808200730.2906102895790.1023346775970.1835151805170.0279562721515-0.02112642466990.1487629721390.01276835228110.1530102663598.206769765256.2164581985719.3871483354
25.30042599492.403058712742.462521409853.387437900241.863533673524.64956244477-0.06972581458160.0893194034829-0.0451641206692-0.01562664338080.1370428505880.0067849000892-0.1488110361750.0795408432146-0.0327122871290.1321743863360.001456669623340.01945658003760.08131843195620.008798413185760.1181880095110.59382151265813.585465068115.1437313511
35.63029806524-2.44839814438-2.56978205112.587446713231.618287037822.439604968720.211958088684-0.07471463189250.427564966756-0.1242569530040.0231649320977-0.252317773355-0.3878499931360.211774586191-0.2381875702020.230133092669-0.03125084220480.02646772256780.146854426587-0.007943105461460.2022778151318.4417829266821.701340098913.1365924717
43.008887776912.99245470433-2.814957823054.22323909362-1.518454101444.50083339004-0.1542545708690.0814917972262-0.176085092204-0.1090325415870.0204448881596-0.02434608444590.4107223294470.09221524891670.1337173495390.1676128872060.0470739826682-0.003080230627250.13415065254-0.000642273200140.1906429723698.332207795595.062468743335.33599747194
53.675251393491.479172636-1.408083164630.741704151908-0.05442300151514.209222485190.02899014746920.1261382228480.0263577646481-0.0361592910004-0.02235416734710.0145609888130.0470084070601-0.200875045215-0.0147067400240.1169157433110.0448914435745-0.00544934283710.1299262417440.01333511338240.1523706826374.0046795248710.78986003244.46563843
64.696336564332.12721472617-3.041235046443.22367412943-0.5818473889962.25176425586-0.03571005496-0.116843631271-0.1953454645730.128051712822-0.148268175564-0.1202581710590.226256842430.2802576237920.1088400751160.1519107680240.03581133585240.00363861769130.108539814333-0.01588778679860.1647259815536.932201219284.329105673578.34717888055
77.71108394611-6.386875872743.690437196445.34446397096-3.040904000113.412599784350.136996659658-0.110806551386-0.26403235214-0.3055623981380.09300395685640.2668783474590.308470528893-0.331789779901-0.2256518685840.250079473755-0.07457987501050.01596878956290.2068766000810.03407678923230.189184550069-7.950283519442.7342541082516.8222217899
83.394217704580.554837035842.490708126010.9036069843160.1803400366946.267070003170.0615766312291-0.3571975368260.0009854406254990.1121740826180.01924635645130.156783613729-0.134636255081-0.693491219077-0.09964511995080.2084090354610.01380303929170.02519734870980.1715813697280.01260322547730.189626497995-5.4721461489512.057081163918.5690123142
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 41 )
2X-RAY DIFFRACTION2chain 'A' and (resid 42 through 64 )
3X-RAY DIFFRACTION3chain 'A' and (resid 65 through 84 )
4X-RAY DIFFRACTION4chain 'A' and (resid 85 through 100 )
5X-RAY DIFFRACTION5chain 'A' and (resid 101 through 122 )
6X-RAY DIFFRACTION6chain 'A' and (resid 123 through 135 )
7X-RAY DIFFRACTION7chain 'A' and (resid 136 through 145 )
8X-RAY DIFFRACTION8chain 'A' and (resid 146 through 164 )

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