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- PDB-3fwv: Crystal Structure of a Redesigned TPR Protein, T-MOD(VMY), in Com... -

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Basic information

Entry
Database: PDB / ID: 3fwv
TitleCrystal Structure of a Redesigned TPR Protein, T-MOD(VMY), in Complex with MEEVF Peptide
Components
  • Heat shock protein HSP 90-beta
  • Hsc70/Hsp90-organizing protein
KeywordsCHAPERONE / tetratricopeptide repeat protein (TPR) / protein-peptide complex / designed protein / TPR / Nucleus / Phosphoprotein / TPR repeat
Function / homology
Function and homology information


: / HSP90-CDC37 chaperone complex / positive regulation of cyclin-dependent protein kinase activity / negative regulation of proteasomal protein catabolic process / Aryl hydrocarbon receptor signalling / aryl hydrocarbon receptor complex / dynein axonemal particle / histone methyltransferase binding / positive regulation of protein localization to cell surface / ATP-dependent protein binding ...: / HSP90-CDC37 chaperone complex / positive regulation of cyclin-dependent protein kinase activity / negative regulation of proteasomal protein catabolic process / Aryl hydrocarbon receptor signalling / aryl hydrocarbon receptor complex / dynein axonemal particle / histone methyltransferase binding / positive regulation of protein localization to cell surface / ATP-dependent protein binding / protein kinase regulator activity / cellular response to interleukin-7 / protein folding chaperone complex / RND1 GTPase cycle / negative regulation of protein metabolic process / positive regulation of tau-protein kinase activity / telomerase holoenzyme complex assembly / Respiratory syncytial virus genome replication / Uptake and function of diphtheria toxin / TPR domain binding / positive regulation of transforming growth factor beta receptor signaling pathway / Assembly and release of respiratory syncytial virus (RSV) virions / dendritic growth cone / positive regulation of phosphoprotein phosphatase activity / Sema3A PAK dependent Axon repulsion / The NLRP3 inflammasome / regulation of protein ubiquitination / HSF1-dependent transactivation / response to unfolded protein / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / telomere maintenance via telomerase / chaperone-mediated protein complex assembly / HSF1 activation / Attenuation phase / cellular response to interleukin-4 / RHOBTB2 GTPase cycle / Purinergic signaling in leishmaniasis infection / axonal growth cone / DNA polymerase binding / supramolecular fiber organization / : / heat shock protein binding / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / nitric-oxide synthase regulator activity / ESR-mediated signaling / positive regulation of cell differentiation / ATP-dependent protein folding chaperone / peptide binding / Hsp90 protein binding / DDX58/IFIH1-mediated induction of interferon-alpha/beta / tau protein binding / placenta development / Regulation of actin dynamics for phagocytic cup formation / kinase binding / histone deacetylase binding / Chaperone Mediated Autophagy / The role of GTSE1 in G2/M progression after G2 checkpoint / regulation of protein localization / positive regulation of nitric oxide biosynthetic process / double-stranded RNA binding / disordered domain specific binding / unfolded protein binding / melanosome / protein folding / MHC class II protein complex binding / cellular response to heat / secretory granule lumen / Estrogen-dependent gene expression / ficolin-1-rich granule lumen / Potential therapeutics for SARS / protein stabilization / protein dimerization activity / regulation of cell cycle / cadherin binding / neuronal cell body / ubiquitin protein ligase binding / Neutrophil degranulation / virion attachment to host cell / negative regulation of apoptotic process / protein kinase binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / perinuclear region of cytoplasm / Golgi apparatus / cell surface / protein homodimerization activity / ATP hydrolysis activity / protein-containing complex / mitochondrion / RNA binding / extracellular exosome / extracellular region / nucleoplasm / ATP binding / identical protein binding / membrane / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
STI1/HOP, DP domain / STI1/HOP, DP domain / Tetratricopeptide repeat 2 / Tetratricopeptide repeat / Heat shock chaperonin-binding / Heat shock chaperonin-binding motif. / TPR repeat / Tetratricopeptide repeat / Tetratricopeptide repeat / Tetratricopeptide repeat domain ...STI1/HOP, DP domain / STI1/HOP, DP domain / Tetratricopeptide repeat 2 / Tetratricopeptide repeat / Heat shock chaperonin-binding / Heat shock chaperonin-binding motif. / TPR repeat / Tetratricopeptide repeat / Tetratricopeptide repeat / Tetratricopeptide repeat domain / Tetratricopeptide repeat / Heat shock protein Hsp90, conserved site / Heat shock hsp90 proteins family signature. / HSP90, C-terminal domain / Heat shock protein Hsp90, N-terminal / Heat shock protein Hsp90 family / Hsp90 protein / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Ribosomal protein S5 domain 2-type fold / Mainly Alpha
Similarity search - Domain/homology
NICKEL (II) ION / Heat shock protein HSP 90-beta / Stress-induced-phosphoprotein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsJackrel, M.E. / Valverde, R. / Regan, L.
CitationJournal: Protein Sci. / Year: 2009
Title: Redesign of a protein-peptide interaction: characterization and applications
Authors: Jackrel, M.E. / Valverde, R. / Regan, L.
History
DepositionJan 19, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 21, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Aug 10, 2011Group: Derived calculations
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Source and taxonomy
Category: database_2 / entity_src_gen ...database_2 / entity_src_gen / pdbx_entity_src_syn / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _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: Hsc70/Hsp90-organizing protein
B: Hsc70/Hsp90-organizing protein
C: Heat shock protein HSP 90-beta
D: Heat shock protein HSP 90-beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0038
Polymers31,7684
Non-polymers2354
Water1,53185
1
A: Hsc70/Hsp90-organizing protein
C: Heat shock protein HSP 90-beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,0014
Polymers15,8842
Non-polymers1172
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1360 Å2
ΔGint-15 kcal/mol
Surface area7620 Å2
MethodPISA
2
B: Hsc70/Hsp90-organizing protein
D: Heat shock protein HSP 90-beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,0014
Polymers15,8842
Non-polymers1172
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1280 Å2
ΔGint-18 kcal/mol
Surface area7600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.604, 66.599, 48.622
Angle α, β, γ (deg.)90.000, 107.210, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Hsc70/Hsp90-organizing protein / Hop / Stress-induced-phosphoprotein 1 / STI1 / Transformation-sensitive protein IEF SSP 3521 / NY- ...Hop / Stress-induced-phosphoprotein 1 / STI1 / Transformation-sensitive protein IEF SSP 3521 / NY-REN-11 antigen


Mass: 15204.315 Da / Num. of mol.: 2 / Fragment: TPR repeats 4-6
Source method: isolated from a genetically manipulated source
Details: Based on the TPR2A domain of the protein HOP from Homo sapiens.
Source: (gene. exp.) Homo sapiens (human) / Gene: STIP1 / Plasmid: pProEx-HTA / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P31948
#2: Protein/peptide Heat shock protein HSP 90-beta / HSP 90 / HSP 84


Mass: 679.781 Da / Num. of mol.: 2 / Fragment: C-terminal residues / Source method: obtained synthetically
Details: The author states that the peptide is a synthetic peptide based on the C-terminal region of the Hsp90 protein, but mutated from the sequence MEEVD in Homo sapiens to MEEVF.
Source: (synth.) synthetic construct (others) / References: UniProt: P08238
#3: Chemical
ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ni
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / 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: 1.83 Å3/Da / Density % sol: 32.81 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 100 mM Tris pH 8.5, 30% PEG MME 2000, 5-10 mM NiCl2, 10% xylitol, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 28, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 11529 / % possible obs: 98.6 % / Redundancy: 5.7 % / Rsym value: 0.053
Reflection shellResolution: 2.2→2.8 Å / Rsym value: 0.187 / % possible all: 87.4

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Processing

Software
NameVersionClassificationNB
REFMAC5.4.0077refinement
PDB_EXTRACT3.006data extraction
RefinementResolution: 2.2→33.3 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.922 / Occupancy max: 1 / Occupancy min: 1 / SU B: 17.134 / SU ML: 0.192 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.485 / ESU R Free: 0.252 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.244 550 4.8 %RANDOM
Rwork0.184 ---
obs0.187 11529 98.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 59.17 Å2 / Biso mean: 17.775 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--2.17 Å20 Å2-0.05 Å2
2---0.32 Å20 Å2
3---2.47 Å2
Refinement stepCycle: LAST / Resolution: 2.2→33.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2232 0 4 85 2321
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0222270
X-RAY DIFFRACTIONr_bond_other_d0.0010.021630
X-RAY DIFFRACTIONr_angle_refined_deg1.2271.9713028
X-RAY DIFFRACTIONr_angle_other_deg1.19733968
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0115262
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.06524.918122
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.08515460
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8491512
X-RAY DIFFRACTIONr_chiral_restr0.0690.2304
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022484
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02456
X-RAY DIFFRACTIONr_mcbond_it0.3311.51332
X-RAY DIFFRACTIONr_mcbond_other0.0761.5534
X-RAY DIFFRACTIONr_mcangle_it0.63922124
X-RAY DIFFRACTIONr_scbond_it1.1893938
X-RAY DIFFRACTIONr_scangle_it1.8974.5904
LS refinement shellResolution: 2.2→2.258 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.372 34 -
Rwork0.214 680 -
all-714 -
obs--83.7 %
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)
16.9359-0.66611.09878.90881.72267.2449-0.06960.0119-0.09920.11330.03750.6579-0.1525-0.57540.03210.0921-0.02180.01550.11920.03890.0888-29.47916.509-1.107
26.0736-1.4407-2.05494.43722.23213.15960.21680.27360.0384-0.2329-0.12370.1051-0.2377-0.118-0.09310.1266-0.0083-0.02860.10520.03980.0476-19.37418.499-5.098
310.48450.26173.379712.30410.1325.91080.0652-0.03760.5496-0.15340.1329-0.5448-0.52330.0241-0.1980.0754-0.0254-0.00540.10060.02850.1219-11.51426.7770.44
45.4544-1.8402-1.05334.46971.30642.7509-0.0363-0.0737-0.39730.1711-0.05250.16680.15940.06490.08880.1006-0.029-0.01840.0840.03170.1211-5.9310.8561.286
518.6688-5.9169-2.488811.8048-8.46389.7585-0.0122-0.191-0.71110.27060.1783-0.58981.45230.5894-0.16620.22150.0023-0.00660.18690.05160.2582.417-2.143-2.236
612.99160.9834-1.738614.60772.02974.5455-0.13040.4809-1.1973-0.80850.15710.64430.6441-0.0596-0.02680.18970.0154-0.030.17990.0050.1619-23.61420.37-27.166
74.64720.52381.12633.81551.26263.36810.0223-0.1606-0.13870.13090.01370.06470.0199-0.1218-0.03610.10990.0160.02420.12740.03130.0541-16.57627.008-19.008
85.2121-1.6115-4.87027.20811.967210.1-0.28410.1538-0.85870.0657-0.0486-0.19971.0507-0.19280.33270.1212-0.00450.02610.19070.03140.2997-4.56519.383-20.692
94.74871.44130.05665.34382.55043.83930.0275-0.26560.07720.0469-0.05270.0995-0.1209-0.11230.02520.08990.03070.01420.10730.01580.04080.04733.113-20.73
102.74791.36920.35666.4780.51087.44960.00640.02210.3534-0.2835-0.0398-0.0476-0.52830.05490.03350.06520.02630.01850.11780.00910.10634.33734.528-27.786
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A222 - 249
2X-RAY DIFFRACTION2A250 - 282
3X-RAY DIFFRACTION3A283 - 294
4X-RAY DIFFRACTION4A295 - 342
5X-RAY DIFFRACTION5A343 - 349
6X-RAY DIFFRACTION6B222 - 231
7X-RAY DIFFRACTION7B232 - 276
8X-RAY DIFFRACTION8B277 - 297
9X-RAY DIFFRACTION9B298 - 320
10X-RAY DIFFRACTION10B321 - 349

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