[English] 日本語
Yorodumi
- PDB-4tw8: The Fk1-Fk2 domains of FKBP52 in complex with iFit-FL -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4tw8
TitleThe Fk1-Fk2 domains of FKBP52 in complex with iFit-FL
ComponentsPeptidyl-prolyl cis-trans isomerase FKBP4
KeywordsISOMERASE / Fk-506 binding domain / Hsp90 cochaperone / immunophiline / peptidyl-prolyl isomerase / ligand selectivity
Function / homology
Function and homology information


steroid hormone receptor complex assembly / negative regulation of microtubule polymerization or depolymerization / male sex differentiation / copper-dependent protein binding / prostate gland development / copper ion transport / nuclear glucocorticoid receptor binding / protein-containing complex localization / negative regulation of microtubule polymerization / FK506 binding ...steroid hormone receptor complex assembly / negative regulation of microtubule polymerization or depolymerization / male sex differentiation / copper-dependent protein binding / prostate gland development / copper ion transport / nuclear glucocorticoid receptor binding / protein-containing complex localization / negative regulation of microtubule polymerization / FK506 binding / androgen receptor signaling pathway / Attenuation phase / axonal growth cone / chaperone-mediated protein folding / heat shock protein binding / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / embryo implantation / ESR-mediated signaling / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / phosphoprotein binding / tau protein binding / negative regulation of neuron projection development / protein folding / protein-macromolecule adaptor activity / Estrogen-dependent gene expression / microtubule / Potential therapeutics for SARS / neuronal cell body / GTP binding / perinuclear region of cytoplasm / protein-containing complex / mitochondrion / RNA binding / extracellular exosome / nucleoplasm / ATP binding / cytosol / cytoplasm
Similarity search - Function
Tetratricopeptide repeat 2 / Tetratricopeptide repeat / : / Chitinase A; domain 3 - #40 / Tetratricopeptide repeat / Chitinase A; domain 3 / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / FKBP-type peptidyl-prolyl cis-trans isomerase domain / FKBP-type peptidyl-prolyl cis-trans isomerase / Peptidyl-prolyl cis-trans isomerase domain superfamily ...Tetratricopeptide repeat 2 / Tetratricopeptide repeat / : / Chitinase A; domain 3 - #40 / Tetratricopeptide repeat / Chitinase A; domain 3 / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / FKBP-type peptidyl-prolyl cis-trans isomerase domain / FKBP-type peptidyl-prolyl cis-trans isomerase / Peptidyl-prolyl cis-trans isomerase domain superfamily / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Chem-37M / Peptidyl-prolyl cis-trans isomerase FKBP4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.003 Å
AuthorsGaali, S. / Kirschner, A. / Cuboni, S. / Hartmann, J. / Kozany, C. / Balsevich, G. / Namendorf, C. / Fernandez-Vizarra, P. / Almeida, O.F.X. / Ruehter, G. ...Gaali, S. / Kirschner, A. / Cuboni, S. / Hartmann, J. / Kozany, C. / Balsevich, G. / Namendorf, C. / Fernandez-Vizarra, P. / Almeida, O.F.X. / Ruehter, G. / Uhr, M. / Schmidt, M.V. / Touma, C. / Bracher, A. / Hausch, F.
Citation
Journal: Nat.Chem.Biol. / Year: 2015
Title: Selective inhibitors of the FK506-binding protein 51 by induced fit.
Authors: Gaali, S. / Kirschner, A. / Cuboni, S. / Hartmann, J. / Kozany, C. / Balsevich, G. / Namendorf, C. / Fernandez-Vizarra, P. / Sippel, C. / Zannas, A.S. / Draenert, R. / Binder, E.B. / ...Authors: Gaali, S. / Kirschner, A. / Cuboni, S. / Hartmann, J. / Kozany, C. / Balsevich, G. / Namendorf, C. / Fernandez-Vizarra, P. / Sippel, C. / Zannas, A.S. / Draenert, R. / Binder, E.B. / Almeida, O.F. / Ruhter, G. / Uhr, M. / Schmidt, M.V. / Touma, C. / Bracher, A. / Hausch, F.
#1: Journal: J. Mol. Biol. / Year: 2013
Title: Crystal structures of the free and ligand-bound FK1-FK2 domain segment of FKBP52 reveal a flexible inter-domain hinge.
Authors: Bracher, A. / Kozany, C. / Hahle, A. / Wild, P. / Zacharias, M. / Hausch, F.
History
DepositionJun 30, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Nov 26, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 10, 2014Group: Database references
Revision 1.2Dec 24, 2014Group: Database references
Revision 1.3Dec 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Peptidyl-prolyl cis-trans isomerase FKBP4
B: Peptidyl-prolyl cis-trans isomerase FKBP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,1184
Polymers52,9402
Non-polymers2,1782
Water181
1
A: Peptidyl-prolyl cis-trans isomerase FKBP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5592
Polymers26,4701
Non-polymers1,0891
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Peptidyl-prolyl cis-trans isomerase FKBP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5592
Polymers26,4701
Non-polymers1,0891
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.654, 46.351, 310.064
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: _ / Auth seq-ID: 21 - 255 / Label seq-ID: 1 - 235

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
Detailsbiological unit is the same as asym.

-
Components

#1: Protein Peptidyl-prolyl cis-trans isomerase FKBP4 / PPIase FKBP4 / 51 kDa FK506-binding protein / FKBP51 / 52 kDa FK506-binding protein / FKBP-52 / 59 ...PPIase FKBP4 / 51 kDa FK506-binding protein / FKBP51 / 52 kDa FK506-binding protein / FKBP-52 / 59 kDa immunophilin / p59 / FK506-binding protein 4 / FKBP-4 / FKBP59 / HSP-binding immunophilin / HBI / Immunophilin FKBP52 / Rotamase


Mass: 26470.018 Da / Num. of mol.: 2 / Fragment: UNP residues 21-255
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FKBP4, FKBP52 / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): codon plus RIL / References: UniProt: Q02790, peptidylprolyl isomerase
#2: Chemical ChemComp-37M / 2-(5-{[({3-[(1R)-1-[({(2S)-1-[(2S)-2-[(1S)-cyclohex-2-en-1-yl]-2-(3,4,5-trimethoxyphenyl)acetyl]piperidin-2-yl}carbonyl)oxy]-3-(3,4-dimethoxyphenyl)propyl]phenoxy}acetyl)amino]methyl}-6-hydroxy-3-oxo-3H-xanthen-9-yl)benzoic acid


Mass: 1089.187 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C63H64N2O15
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.1 Å3/Da / Density % sol: 60.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 28 % PEG-6000, 2 % DMSO and TrisHCl pH 8.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 9, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.003→155.032 Å / Num. all: 13725 / Num. obs: 13725 / % possible obs: 97.8 % / Redundancy: 6 % / Rpim(I) all: 0.062 / Rrim(I) all: 0.157 / Rsym value: 0.143 / Net I/av σ(I): 5 / Net I/σ(I): 10.2 / Num. measured all: 81673
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
3-3.174.70.7591850317910.3570.759291
3.17-3.365.20.5181.5942518250.2390.5183.196.6
3.36-3.595.30.2992.6929617650.1390.2995.497.8
3.59-3.886.10.2233.4997416460.0960.2237.799.3
3.88-4.256.80.1415.41048415470.0580.1411299.8
4.25-4.756.90.1027.2955013940.0410.10216.799.9
4.75-5.486.40.1017.2804112600.0430.10115.3100
5.48-6.7170.1047.2766010910.0420.10414.6100
6.71-9.56.50.06510.257128810.0270.06520.199.9
9.5-46.3515.80.04512.530285250.020.04526.999.2

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3.19 Å45.84 Å
Translation3.19 Å45.84 Å

-
Processing

Software
NameVersionClassification
SCALA3.3.16data scaling
MOLREP10.2.35phasing
PDB_EXTRACT3.14data extraction
REFMAC5.7.0029refinement
XDSdata reduction
XSCALEdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Q1C

1q1c


Resolution: 3.003→30 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.87 / WRfactor Rfree: 0.2337 / WRfactor Rwork: 0.1832 / FOM work R set: 0.8207 / SU B: 45.383 / SU ML: 0.355 / SU R Cruickshank DPI: 0.3655 / SU Rfree: 0.4307 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.431 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2569 674 4.9 %RANDOM
Rwork0.2099 12971 --
obs0.2122 13645 97.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 124.58 Å2 / Biso mean: 55.192 Å2 / Biso min: 22.8 Å2
Baniso -1Baniso -2Baniso -3
1--0.44 Å20 Å20 Å2
2--0.68 Å20 Å2
3----0.24 Å2
Refinement stepCycle: final / Resolution: 3.003→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3698 0 142 1 3841
Biso mean--81.05 22.8 -
Num. residues----470
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.023936
X-RAY DIFFRACTIONr_angle_refined_deg1.1572.025312
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5515468
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.72324.719178
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.98915669
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3221519
X-RAY DIFFRACTIONr_chiral_restr0.0750.2542
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213021
Refine LS restraints NCS

Ens-ID: 1 / Number: 245 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.15 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 3.003→3.08 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.38 41 -
Rwork0.352 829 -
all-870 -
obs--85.21 %
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)
16.28060.08850.08124.30360.66094.4957-0.067-0.02590.1959-0.02150.2284-0.2350.30390.3121-0.16140.2774-0.01060.01170.18730.00940.11717.6995-9.906851.943
25.6775-2.0751-0.22075.10370.92174.46010.0589-0.198-0.15050.00840.09720.07080.03690.2003-0.15610.021-0.01970.03890.0412-0.01280.2183-11.6057-1.612176.892
311.28721.24543.41110.14350.37881.03310.1752-0.02910.12680.0904-0.11360.02810.11950.0044-0.06160.81370.10410.08590.4591-0.11310.46516.7859-20.647755.4968
44.411.84080.01885.7299-0.37635.9391-0.0692-0.09810.0043-0.09440.04130.10220.3826-0.42970.02790.3285-0.02570.03830.1737-0.0230.18720.3637-15.338628.1726
54.8706-1.88910.04895.31020.17134.4921-0.08060.16680.1093-0.14750.04780.134-0.09260.01690.03280.3511-0.0841-0.01130.03110.03880.18036.32970.36920.5104
60.0845-0.7211-1.45886.870813.788827.7232-0.11170.01590.0380.09170.3185-0.03460.37870.7558-0.20680.9122-0.0207-0.31790.74550.06270.41989.4566-22.089426.1065
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A21 - 139
2X-RAY DIFFRACTION2A140 - 255
3X-RAY DIFFRACTION3C1
4X-RAY DIFFRACTION4B21 - 139
5X-RAY DIFFRACTION5B140 - 255
6X-RAY DIFFRACTION6D1

+
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