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- PDB-5tth: Heterodimeric SpyCatcher/SpyTag-fused zebrafish TRAP1 in ATP/ADP-... -

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Basic information

Entry
Database: PDB / ID: 5tth
TitleHeterodimeric SpyCatcher/SpyTag-fused zebrafish TRAP1 in ATP/ADP-hybrid state
Components
  • C-terminal SpyCatcher fusion of wildtype zebrafish TNF receptor-associated protein 1
  • C-terminal Spytag fusion of R417A zebrafish TNF receptor-associated protein 1
KeywordsCHAPERONE / Hsp90 / ATP / Trap1 / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


Citric acid cycle (TCA cycle) / ATP-dependent protein folding chaperone / unfolded protein binding / protein folding / mitochondrial inner membrane / mitochondrial matrix / calcium ion binding / protein kinase binding / magnesium ion binding / ATP hydrolysis activity ...Citric acid cycle (TCA cycle) / ATP-dependent protein folding chaperone / unfolded protein binding / protein folding / mitochondrial inner membrane / mitochondrial matrix / calcium ion binding / protein kinase binding / magnesium ion binding / ATP hydrolysis activity / ATP binding / identical protein binding
Similarity search - Function
Heat shock protein 90, C-terminal domain / Fibronectin binding repeat / Collagen-binding surface protein Cna-like, B-type domain / Fibronectin binding repeat / Cna protein B-type domain / Uncharacterised domain CHP03934, TQXA / Rossmann fold - #11260 / Thioester domain / Thioester domain / Ribosomal Protein S5; domain 2 - #80 ...Heat shock protein 90, C-terminal domain / Fibronectin binding repeat / Collagen-binding surface protein Cna-like, B-type domain / Fibronectin binding repeat / Cna protein B-type domain / Uncharacterised domain CHP03934, TQXA / Rossmann fold - #11260 / Thioester domain / Thioester domain / Ribosomal Protein S5; domain 2 - #80 / Prealbumin-like fold domain / Prealbumin-like fold domain / Histidine kinase/HSP90-like ATPase / Ribosomal Protein S5; domain 2 / Histidine kinase-like ATPase, C-terminal domain / HSP90, C-terminal domain / Heat shock protein Hsp90, N-terminal / Heat shock protein Hsp90 family / Hsp90 protein / Heat Shock Protein 90 / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Four Helix Bundle (Hemerythrin (Met), subunit A) / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase superfamily / Ribosomal protein S5 domain 2-type fold / Immunoglobulin-like fold / Immunoglobulins / Up-down Bundle / Immunoglobulin-like / Sandwich / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / BERYLLIUM TRIFLUORIDE ION / Heat shock protein 75 kDa, mitochondrial / Fibronectin binding protein
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
Streptococcus pyogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsElnatan, D. / Betegon, M. / Liu, Y. / Agard, D.A. / Northeast Structural Genomics Consortium (NESG)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U01 GM098254. United States
CitationJournal: Elife / Year: 2017
Title: Symmetry broken and rebroken during the ATP hydrolysis cycle of the mitochondrial Hsp90 TRAP1.
Authors: Elnatan, D. / Betegon, M. / Liu, Y. / Ramelot, T. / Kennedy, M.A. / Agard, D.A.
History
DepositionNov 3, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 23, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2May 8, 2019Group: Data collection / Database references / Category: citation_author / Item: _citation_author.identifier_ORCID
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_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.value / _struct_conn.pdbx_dist_value / _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
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: C-terminal SpyCatcher fusion of wildtype zebrafish TNF receptor-associated protein 1
B: C-terminal Spytag fusion of R417A zebrafish TNF receptor-associated protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,3028
Polymers160,2672
Non-polymers1,0356
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14520 Å2
ΔGint-104 kcal/mol
Surface area58580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)180.086, 95.711, 126.558
Angle α, β, γ (deg.)90.000, 134.590, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein C-terminal SpyCatcher fusion of wildtype zebrafish TNF receptor-associated protein 1 / Trap1 protein


Mass: 83827.672 Da / Num. of mol.: 1 / Mutation: I734E and M769Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish), (gene. exp.) Streptococcus pyogenes (bacteria)
Gene: trap1, fba2 / Plasmid: pet151DTOPO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-RIL / References: UniProt: A8WFV1, UniProt: Q8G9G1
#2: Protein C-terminal Spytag fusion of R417A zebrafish TNF receptor-associated protein 1 / Trap1 protein


Mass: 76439.688 Da / Num. of mol.: 1 / Mutation: R417A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish), (gene. exp.) Streptococcus pyogenes (bacteria)
Gene: trap1, fba2 / Plasmid: pet151DTOPO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-RIL / References: UniProt: A8WFV1, UniProt: Q8G9G1
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: BeF3
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
Has protein modificationY

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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: 2.6 Å3/Da / Density % sol: 53 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 0.19 M potassium acetate, 20-22% PEG3350, Benzamidine hydrochloride (5-25 mM)

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Data collection

DiffractionMean temperature: 91.4 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11587 Å / Relative weight: 1
ReflectionResolution: 3.2→90.13 Å / Num. obs: 21244 / % possible obs: 83 % / Redundancy: 2.5 % / Rsym value: 0.146 / Net I/σ(I): 9.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4J0B

4j0b


Resolution: 3.2→49 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.883 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.65
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.261 1014 4.8 %RANDOM
Rwork0.2284 ---
obs0.2299 21154 82.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 300.94 Å2 / Biso mean: 126.776 Å2 / Biso min: 38.03 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20.35 Å2
2---1.62 Å20 Å2
3---0.33 Å2
Refinement stepCycle: LAST / Resolution: 3.2→49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10351 0 64 0 10415
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01910642
X-RAY DIFFRACTIONr_bond_other_d00.0210214
X-RAY DIFFRACTIONr_angle_refined_deg1.491.97114364
X-RAY DIFFRACTIONr_angle_other_deg3.596323511
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0151291
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.92923.992506
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.678151950
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1961579
X-RAY DIFFRACTIONr_chiral_restr0.0860.21603
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211853
X-RAY DIFFRACTIONr_gen_planes_other0.0070.022438
X-RAY DIFFRACTIONr_mcbond_it2.928.625167
X-RAY DIFFRACTIONr_mcbond_other2.928.6185166
X-RAY DIFFRACTIONr_mcangle_it4.99312.9136439
LS refinement shellResolution: 3.197→3.28 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.393 79 -
Rwork0.357 1403 -
all-1482 -
obs--80.28 %
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)
14.89110.397-1.23870.993-0.23070.93920.20510.62260.4401-0.4784-0.1247-0.0134-0.05140.1266-0.08050.48020.1431-0.17920.23740.01730.2751-35.818.874-18.689
23.67930.2717-0.67566.9282-1.14642.22130.15270.3570.0757-0.5548-0.02260.6027-0.0599-0.2218-0.130.24470.0265-0.24440.118-0.00520.2728-54.164.392-16.654
33.43411.87673.52622.84073.97386.11220.099-0.23720.0280.2856-0.24330.3240.2779-0.3680.14420.2731-0.01760.02430.0288-0.01060.4547-46.38112.3248.977
43.15370.583.1120.72390.71035.2865-0.27260.00660.43610.39030.034-0.2256-0.47260.72670.23850.5377-0.0374-0.18010.27290.03640.4474-24.28624.80125.231
53.35811.51982.80992.7056-1.04927.73090.33580.21490.1375-0.3156-0.2906-0.337-0.01940.6855-0.04520.749-0.08150.04550.7459-0.04120.5104-7.88210.96556.297
68.9331.1396-1.812.59890.84130.8445-0.26020.0309-0.5893-0.0130.1018-0.06580.07720.05550.15840.6141-0.1226-0.10710.4426-0.04130.3002-16.8970.91656.44
77.77011.71921.27617.40471.24192.44760.2526-0.04750.3226-0.2296-0.1518-0.5496-0.0486-0.0039-0.10070.7585-0.06010.05260.72460.02780.30057.8433.80982.413
83.07570.14640.75421.6381-0.31681.09440.01950.69790.3558-0.4602-0.1947-0.1116-0.00570.23640.17520.33970.07260.00440.23870.00570.2407-18.8964.731-17.152
97.59731.3241-0.51824.2664-0.1077.27460.33050.25090.2852-0.518-0.2273-0.012-0.4243-0.632-0.10310.14990.0764-0.06110.08080.04210.2588-20.159-5.4196.735
101.9174-4.87674.321612.4201-10.99749.74680.08920.01230.0041-0.2715-0.1032-0.06840.25610.03960.01390.5153-0.02350.11670.54110.03050.6066-31.2960.201-3.848
111.24890.2837-1.67440.64870.50246.3444-0.0126-0.17-0.01040.23270.02810.11640.0934-0.1904-0.01560.28240.072-0.11810.16250.02220.3147-28.99-11.3143.718
125.6223-0.58212.03472.1170.1146.95-0.73770.70180.6145-0.15720.5951-0.2803-1.08580.55910.14260.552-0.05850.07370.62930.04060.56168.3039.74189.793
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A85 - 150
2X-RAY DIFFRACTION2A151 - 277
3X-RAY DIFFRACTION3A278 - 411
4X-RAY DIFFRACTION4A412 - 588
5X-RAY DIFFRACTION5A589 - 679
6X-RAY DIFFRACTION6A680 - 717
7X-RAY DIFFRACTION7A722 - 803
8X-RAY DIFFRACTION8B85 - 340
9X-RAY DIFFRACTION9B341 - 414
10X-RAY DIFFRACTION10B415 - 424
11X-RAY DIFFRACTION11B425 - 717
12X-RAY DIFFRACTION12B722 - 737

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