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- PDB-2xgy: Complex of Rabbit Endogenous Lentivirus (RELIK)Capsid with Cyclop... -

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Basic information

Entry
Database: PDB / ID: 2xgy
TitleComplex of Rabbit Endogenous Lentivirus (RELIK)Capsid with Cyclophilin A
Components
  • PEPTIDYL-PROLYL CIS-TRANS ISOMERASE A
  • RELIK CAPSID N-TERMINAL DOMAIN
KeywordsVIRAL PROTEIN/ISOMERASE / VIRAL PROTEIN-ISOMERASE COMPLEX / RETROVIRAL CAPSID / ENDOGENOUS
Function / homology
Function and homology information


negative regulation of protein K48-linked ubiquitination / regulation of apoptotic signaling pathway / cell adhesion molecule production / lipid droplet organization / negative regulation of viral life cycle / heparan sulfate binding / regulation of viral genome replication / leukocyte chemotaxis / virion binding / negative regulation of stress-activated MAPK cascade ...negative regulation of protein K48-linked ubiquitination / regulation of apoptotic signaling pathway / cell adhesion molecule production / lipid droplet organization / negative regulation of viral life cycle / heparan sulfate binding / regulation of viral genome replication / leukocyte chemotaxis / virion binding / negative regulation of stress-activated MAPK cascade / endothelial cell activation / Basigin interactions / protein peptidyl-prolyl isomerization / 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 / negative regulation of protein phosphorylation / APOBEC3G mediated resistance to HIV-1 infection / viral release from host cell / Calcineurin activates NFAT / activation of protein kinase B activity / Binding and entry of HIV virion / positive regulation of viral genome replication / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / negative regulation of protein kinase activity / neutrophil chemotaxis / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / positive regulation of protein secretion / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / Assembly Of The HIV Virion / : / Budding and maturation of HIV virion / platelet activation / platelet aggregation / integrin binding / positive regulation of protein phosphorylation / neuron differentiation / SARS-CoV-1 activates/modulates innate immune responses / unfolded protein binding / Platelet degranulation / protein folding / cellular response to oxidative stress / secretory granule lumen / vesicle / ficolin-1-rich granule lumen / positive regulation of MAPK cascade / focal adhesion / apoptotic process / Neutrophil degranulation / protein-containing complex / extracellular space / RNA binding / extracellular exosome / extracellular region / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
Human Immunodeficiency Virus Type 1 Capsid Protein / Human Immunodeficiency Virus Type 1 Capsid Protein / 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 ...Human Immunodeficiency Virus Type 1 Capsid Protein / Human Immunodeficiency Virus Type 1 Capsid Protein / 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 / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Peptidyl-prolyl cis-trans isomerase A
Similarity search - Component
Biological speciesORYCTOLAGUS CUNICULUS (rabbit)
HOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsGoldstone, D.C. / Robertson, L.E. / Haire, L.F. / Stoye, J.P. / Taylor, I.A.
CitationJournal: Cell Host Microbe / Year: 2010
Title: Structural and Functional Analysis of Prehistoric Lentiviruses Uncovers an Ancient Molecular Interface.
Authors: Goldstone, D.C. / Yap, M.W. / Robertson, L.E. / Haire, L.F. / Taylor, W.R. / Katzourakis, A. / Stoye, J.P. / Taylor, I.A.
History
DepositionJun 8, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 22, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RELIK CAPSID N-TERMINAL DOMAIN
B: PEPTIDYL-PROLYL CIS-TRANS ISOMERASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5174
Polymers35,3332
Non-polymers1842
Water6,612367
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1890 Å2
ΔGint-5.1 kcal/mol
Surface area13280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.158, 117.158, 49.655
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein RELIK CAPSID N-TERMINAL DOMAIN


Mass: 16511.818 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ORYCTOLAGUS CUNICULUS (rabbit) / Description: SYNTHESISED RECONSTRUCTED GENE / Plasmid: PET22B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
#2: Protein PEPTIDYL-PROLYL CIS-TRANS ISOMERASE A / PPIASE A / ROTAMASE A / CYCLOPHILIN A / CYCLOSPORIN A-BINDING PROTEIN


Mass: 18821.359 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGEX-6P1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P62937, peptidylprolyl isomerase
#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.: 367 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUES 141-149 ARE AN EXPRESSION TAG.

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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: 2.07 Å3/Da / Density % sol: 45 % / Description: NONE
Crystal growpH: 7.5 / Details: 16-26% PEG3350, 0.1M HEPES PH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→25 Å / Num. obs: 35238 / % possible obs: 96.8 % / Observed criterion σ(I): 2 / Redundancy: 21.2 % / Biso Wilson estimate: 30.39 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 71.4
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 11.8 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 4.4 / % possible all: 94.1

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→24.482 Å / SU ML: 0.31 / σ(F): 1.34 / Phase error: 17.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1874 1756 5 %
Rwork0.1558 --
obs0.1574 35141 96.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 57.894 Å2 / ksol: 0.366 e/Å3
Displacement parametersBiso mean: 35.1 Å2
Baniso -1Baniso -2Baniso -3
1-1.6015 Å2-0 Å2-0 Å2
2--1.6015 Å2-0 Å2
3----3.2031 Å2
Refinement stepCycle: LAST / Resolution: 1.8→24.482 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2237 0 12 367 2616
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052300
X-RAY DIFFRACTIONf_angle_d0.9313108
X-RAY DIFFRACTIONf_dihedral_angle_d15.66828
X-RAY DIFFRACTIONf_chiral_restr0.063337
X-RAY DIFFRACTIONf_plane_restr0.004405
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.84870.28441260.212479X-RAY DIFFRACTION93
1.8487-1.9030.19141390.17282463X-RAY DIFFRACTION94
1.903-1.96440.20541280.15392533X-RAY DIFFRACTION96
1.9644-2.03460.19131290.14862491X-RAY DIFFRACTION95
2.0346-2.1160.16581150.14732545X-RAY DIFFRACTION96
2.116-2.21230.20151390.14452533X-RAY DIFFRACTION97
2.2123-2.32880.17911420.1452554X-RAY DIFFRACTION97
2.3288-2.47460.18141370.14872565X-RAY DIFFRACTION97
2.4746-2.66550.19591380.15462600X-RAY DIFFRACTION98
2.6655-2.93330.19631350.15082607X-RAY DIFFRACTION98
2.9333-3.35680.18581460.15422621X-RAY DIFFRACTION99
3.3568-4.22570.16551310.13032666X-RAY DIFFRACTION99
4.2257-24.48450.17121510.15752728X-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)
12.03592.0048-1.52615.44021.26392.80440.04680.5799-0.42781.2256-0.5864-1.3691-1.27140.11460.81720.4612-0.2357-0.10710.35950.06080.640543.4717-22.90686.5899
24.00562.20230.8577-1.63661.07721.35690.3663-0.15711.02960.1998-0.22990.307-0.4961-0.1128-0.07970.5874-0.04460.13880.2021-0.02520.441128.7404-11.47154.744
31.7247-0.94710.04421.9118-0.11820.1027-0.08680.2772-0.2254-0.2230.04020.1692-0.204-0.00390.03120.3961-0.01270.07780.22120.06220.287627.4403-18.4287-2.2514
43.97411.8723-1.15033.9525-5.01182.8932-0.19480.5239-0.05390.0366-0.1351-0.6505-0.35750.5450.27760.321-0.09360.04490.30180.02570.275735.7494-25.61245.6862
55.8112-2.4543-2.1156.96622.57184.1186-0.2231-0.76870.53981.4475-0.0250.4816-0.35380.20410.12010.4635-0.04450.12360.3179-0.04670.310927.6935-20.255410.3625
63.4981-2.2358-4.23534.03270.73333.72060.78640.3931.0540.223-0.12650.9789-0.1259-0.9991-0.62730.34120.0240.19030.32840.0120.556516.9115-21.70867.4965
7-0.48051.5853-0.47657.2978-0.98431.0687-0.08370.0941-0.05790.04370.15570.86390.1671-0.351-0.06420.2347-0.05590.02210.29860.0010.276421.0842-37.95.2292
8-0.1985-0.5627-0.07962.95271.2942-0.7823-0.0305-0.2074-0.11260.7342-0.0664-0.00040.10220.09780.07650.3335-0.03720.03740.3060.04750.261831.6601-42.607411.4796
9-4.3971-1.6483-3.49067.71662.16862.54160.1832-0.0315-0.1844-0.15050.159-1.74320.17330.756-0.30260.2041-0.0728-0.02690.312-0.0270.420141.0684-35.1327.6854
10-0.0498-0.42170.04061.38080.56520.1862-0.01520.04090.0745-0.31920.10180.0992-0.1256-0.0909-0.08180.2602-0.04550.03850.22340.0280.238926.3751-29.1643-0.7039
11-1.0731-1.2260.09520.9011-0.25311.96320.13810.1231-0.1976-0.0728-0.0895-0.24190.19340.4533-0.04490.21660.0192-0.03450.31970.01640.248246.1666-64.58870.4794
120.9995-0.24690.2871-0.11780.47080.63560.1271-0.134-0.13840.0064-0.04590.01510.0708-0.0438-0.08630.258-0.0371-0.06370.20890.02790.244736.6696-62.87915.4094
13-0.2585-0.1509-0.0280.322-0.23611.4365-0.0073-0.1239-0.2062-0.01470.09250.00140.1827-0.0884-0.07070.2566-0.1005-0.04210.33160.03940.263338.4237-65.397914.507
141.88231.36040.86372.30010.6897-0.12660.0982-0.4194-0.09420.5991-0.3796-0.1199-0.21530.09530.21810.3254-0.1012-0.05430.41710.03830.258946.5584-58.083117.7927
150.52-0.1911-0.08260.29170.0156-0.52050.1116-0.00290.09680.0991-0.1596-0.0679-0.06160.10640.04060.2777-0.0583-0.03290.26140.02080.245743.4762-52.92266.6253
161.2396-0.1461-0.86990.52461.28072.75220.3963-0.12440.10390.24970.0152-0.3716-0.45640.0988-0.30670.2856-0.05060.00790.2426-0.00170.314640.461-45.12295.4279
170.0177-0.11150.04080.7069-0.3134-0.42440.09990.095-0.1189-0.1897-0.1078-0.0834-0.01150.14310.02190.2588-0.0021-0.03950.28630.00010.214439.653-58.3713-5.2308
181.2025-0.30250.51570.7805-0.08620.78630.28480.1081-0.1854-0.0687-0.19080.17710.0710.024-0.08590.2470.0019-0.04870.2226-0.01780.265132.7857-64.48820.0579
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 1:14)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 15:29)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 30:45)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 46:52)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 53:60)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 61:69)
7X-RAY DIFFRACTION7(CHAIN A AND RESID 70:85)
8X-RAY DIFFRACTION8(CHAIN A AND RESID 86:109)
9X-RAY DIFFRACTION9(CHAIN A AND RESID 110:118)
10X-RAY DIFFRACTION10(CHAIN A AND RESID 119:136)
11X-RAY DIFFRACTION11(CHAIN B AND RESID 2:42)
12X-RAY DIFFRACTION12(CHAIN B AND RESID 43:65)
13X-RAY DIFFRACTION13(CHAIN B AND RESID 66:79)
14X-RAY DIFFRACTION14(CHAIN B AND RESID 80:85)
15X-RAY DIFFRACTION15(CHAIN B AND RESID 86:117)
16X-RAY DIFFRACTION16(CHAIN B AND RESID 118:126)
17X-RAY DIFFRACTION17(CHAIN B AND RESID 127:144)
18X-RAY DIFFRACTION18(CHAIN B AND RESID 145:165)

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