[English] 日本語
Yorodumi
- PDB-4dgc: TRIMCyp cyclophilin domain from Macaca mulatta: cyclosporin A complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4dgc
TitleTRIMCyp cyclophilin domain from Macaca mulatta: cyclosporin A complex
Components
  • TRIMCyp
  • cyclosporin A
KeywordsISOMERASE/IMMUNOSUPPRESSANT / anti-viral protein / ISOMERASE-IMMUNOSUPPRESSANT complex
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 / negative regulation of stress-activated MAPK cascade / endothelial cell activation ...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 / negative regulation of stress-activated MAPK cascade / endothelial cell activation / protein peptidyl-prolyl isomerization / cyclosporin A binding / negative regulation of protein phosphorylation / activation of protein kinase B activity / positive regulation of viral genome replication / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / negative regulation of protein kinase activity / neutrophil chemotaxis / positive regulation of protein secretion / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / positive regulation of NF-kappaB transcription factor activity / RING-type E3 ubiquitin transferase / platelet activation / autophagy / platelet aggregation / integrin binding / positive regulation of protein phosphorylation / protein folding / cellular response to oxidative stress / defense response to virus / positive regulation of MAPK cascade / protein ubiquitination / innate immune response / apoptotic process / protein-containing complex / extracellular region / zinc ion binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Zinc finger, RING-type, eukaryotic / RING-type zinc-finger / Cyclophilin-like / B-box zinc finger / Cyclophilin / B-Box-type zinc finger / B-box-type zinc finger / Zinc finger B-box type profile. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, conserved site ...Zinc finger, RING-type, eukaryotic / RING-type zinc-finger / Cyclophilin-like / B-box zinc finger / Cyclophilin / B-Box-type zinc finger / B-box-type zinc finger / Zinc finger B-box type profile. / 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 / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Cyclosporin A / : / Peptidyl-prolyl cis-trans isomerase A / Peptidyl-prolyl cis-trans isomerase A
Similarity search - Component
Biological speciesMacaca mulatta (Rhesus monkey)
Tolypocladium inflatum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsCaines, M.E.C. / Bichel, K. / Price, A.J. / McEwan, W.A. / James, L.C.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2012
Title: Diverse HIV viruses are targeted by a conformationally dynamic antiviral.
Authors: Caines, M.E. / Bichel, K. / Price, A.J. / McEwan, W.A. / Towers, G.J. / Willett, B.J. / Freund, S.M. / James, L.C.
History
DepositionJan 25, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 8, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 28, 2012Group: Database references
Revision 1.2Apr 18, 2012Group: Database references
Revision 1.3Feb 27, 2013Group: Other
Revision 1.4Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.5Dec 6, 2023Group: Data collection / Derived calculations / Category: chem_comp_atom / chem_comp_bond / struct_conn
Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: TRIMCyp
B: TRIMCyp
C: TRIMCyp
D: TRIMCyp
E: TRIMCyp
F: cyclosporin A
G: cyclosporin A
H: cyclosporin A
I: cyclosporin A
J: cyclosporin A


Theoretical massNumber of molelcules
Total (without water)96,18510
Polymers96,18510
Non-polymers00
Water4,900272
1
A: TRIMCyp
F: cyclosporin A


Theoretical massNumber of molelcules
Total (without water)19,2372
Polymers19,2372
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area920 Å2
ΔGint-8 kcal/mol
Surface area8290 Å2
MethodPISA
2
B: TRIMCyp
G: cyclosporin A


Theoretical massNumber of molelcules
Total (without water)19,2372
Polymers19,2372
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area920 Å2
ΔGint-8 kcal/mol
Surface area8030 Å2
MethodPISA
3
C: TRIMCyp
H: cyclosporin A


Theoretical massNumber of molelcules
Total (without water)19,2372
Polymers19,2372
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area930 Å2
ΔGint-8 kcal/mol
Surface area8160 Å2
MethodPISA
4
D: TRIMCyp
I: cyclosporin A


Theoretical massNumber of molelcules
Total (without water)19,2372
Polymers19,2372
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area860 Å2
ΔGint-6 kcal/mol
Surface area8130 Å2
MethodPISA
5
E: TRIMCyp
J: cyclosporin A


Theoretical massNumber of molelcules
Total (without water)19,2372
Polymers19,2372
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area890 Å2
ΔGint-6 kcal/mol
Surface area8030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.470, 108.470, 423.060
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E

NCS domain segments:

Ens-ID: 1 / Refine code: 4

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11VALVALPHEPHEAA2 - 672 - 67
21VALVALPHEPHEBB2 - 672 - 67
31VALVALPHEPHECC2 - 672 - 67
41VALVALPHEPHEDD2 - 672 - 67
51VALVALPHEPHEEE2 - 672 - 67
12SERSERLEULEUAA77 - 16477 - 164
22SERSERLEULEUBB77 - 16477 - 164
32SERSERLEULEUCC77 - 16477 - 164
42SERSERLEULEUDD77 - 16477 - 164
52SERSERLEULEUEE77 - 16477 - 164

-
Components

#1: Protein
TRIMCyp / Peptidyl-prolyl cis-trans isomerase


Mass: 18016.473 Da / Num. of mol.: 5 / Fragment: cyclophilin domain (UNP residues 304-468)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Gene: TRIMCyp / Plasmid: pOPT / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3)
References: UniProt: B0LJC8, UniProt: P62940*PLUS, peptidylprolyl isomerase
#2: Protein/peptide
cyclosporin A


Type: Cyclic peptide / Class: Immunosuppressant / Mass: 1220.625 Da / Num. of mol.: 5 / Source method: obtained synthetically
Details: CYCLOSPORIN IS A CYCLIC UNDECAPEPTIDE. CYCLIZATION IS ACHIEVED BY LINKING THE N- AND THE C- TERMINI.
Source: (synth.) Tolypocladium inflatum (fungus) / References: NOR: NOR00033, Cyclosporin A
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 272 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCYCLOSPORIN IS A CYCLIC UNDECAPEPTIDE. HERE, CYCLOSPORIN A IS REPRESENTED BY THE SEQUENCE (SEQRES) ...CYCLOSPORIN IS A CYCLIC UNDECAPEPTIDE. HERE, CYCLOSPORIN A IS REPRESENTED BY THE SEQUENCE (SEQRES) GROUP: 1 NAME: CYCLOSPORIN A CHAIN: F, G, H, I, J COMPONENT_1: PEPTIDE LIKE SEQUENCE RESIDUES 1 TO 11 DESCRIPTION: CYCLOSPORIN IS A CYCLIC UNDECAPEPTIDE. CYCLIZATION IS ACHIEVED BY LINKING THE N- AND THE C- TERMINI.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.73 Å3/Da / Density % sol: 67.07 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 2.05 M ammonium sulfate, 10 MM magnesium sulfate, 0.1 M Bis-Tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.072 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 24, 2010
RadiationMonochromator: single crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.072 Å / Relative weight: 1
ReflectionResolution: 2.65→93.938 Å / Num. all: 41285 / Num. obs: 41285 / % possible obs: 94.9 % / Redundancy: 3.6 % / Biso Wilson estimate: 58.64 Å2 / Rsym value: 0.07 / Net I/σ(I): 12.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.65-2.793.20.2223.31952661050.22298.2
2.79-2.963.60.164.52104657940.1698.4
2.96-3.173.60.1175.91979854500.11798.1
3.17-3.423.70.0838.21851550510.08397
3.42-3.753.70.06410.21687646140.06495.9
3.75-4.193.70.05412.21518341290.05494.4
4.19-4.843.70.05411.51323136050.05492.5
4.84-5.933.70.0757.71106429910.07589.4
5.93-8.383.40.05410.3772522450.05483.8
8.38-78.183.80.04114.4492113010.04179.5

-
Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
PXSOFTdata collection
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WLW

2wlw


Resolution: 2.65→93.938 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.923 / WRfactor Rfree: 0.219 / WRfactor Rwork: 0.1836 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8853 / SU B: 12.683 / SU ML: 0.154 / SU R Cruickshank DPI: 0.3815 / SU Rfree: 0.2488 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.381 / ESU R Free: 0.249 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2158 2086 5.1 %RANDOM
Rwork0.1818 ---
obs0.1835 41077 93.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 111.4 Å2 / Biso mean: 43.0877 Å2 / Biso min: 12.53 Å2
Baniso -1Baniso -2Baniso -3
1-0.21 Å20.1 Å20 Å2
2--0.21 Å20 Å2
3----0.31 Å2
Refinement stepCycle: LAST / Resolution: 2.65→93.938 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6532 0 0 272 6804
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0226665
X-RAY DIFFRACTIONr_bond_other_d0.0010.024562
X-RAY DIFFRACTIONr_angle_refined_deg1.4081.9758963
X-RAY DIFFRACTIONr_angle_other_deg0.872311132
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0655815
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.36624.373279
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.24151078
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.0181525
X-RAY DIFFRACTIONr_chiral_restr0.0840.2960
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0217454
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021364
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 2032 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
AMEDIUM POSITIONAL0.240.5
BMEDIUM POSITIONAL0.220.5
CMEDIUM POSITIONAL0.280.5
DMEDIUM POSITIONAL0.220.5
EMEDIUM POSITIONAL0.250.5
AMEDIUM THERMAL2.222
BMEDIUM THERMAL1.772
CMEDIUM THERMAL1.122
DMEDIUM THERMAL1.62
EMEDIUM THERMAL1.62
LS refinement shellResolution: 2.65→2.719 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 149 -
Rwork0.308 2634 -
all-2783 -
obs--95.34 %
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)
14.1238-0.08150.68412.90811.1092.62240.11280.0588-0.21530.0255-0.09160.14910.054-0.1706-0.02120.0305-0.00160.00020.1875-0.06410.040541.6458-39.126218.0266
23.201-0.0120.72532.08221.34582.90970.0459-0.03530.0944-0.01860.1204-0.1468-0.02690.1651-0.16630.06250.0125-0.04930.3001-0.09560.080222.4251-50.7583-7.4794
33.39790.14050.26863.98460.39712.57220.030.03210.43530.0004-0.02610.43-0.5548-0.3187-0.00380.3110.09510.04830.13160.00140.183238.1511-4.931131.7791
43.14410.27270.43233.97221.08672.0760.0006-0.0791-0.0550.04850.2422-0.74270.01980.6865-0.24280.11520.0604-0.06580.7046-0.2260.4027-8.8774-37.962439.8269
53.02050.2863-0.56453.88370.72282.90090.15670.06130.2988-0.410.1602-0.7422-0.27980.7328-0.31690.3162-0.23010.25940.5411-0.18840.4219-13.4907-12.407715.6746
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 164
2X-RAY DIFFRACTION2B2 - 165
3X-RAY DIFFRACTION3C2 - 164
4X-RAY DIFFRACTION4D2 - 164
5X-RAY DIFFRACTION5E2 - 164

+
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://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