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- PDB-2o1v: Structure of full length GRP94 with ADP bound -

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Basic information

Entry
Database: PDB / ID: 2o1v
TitleStructure of full length GRP94 with ADP bound
ComponentsEndoplasmin
KeywordsCHAPERONE / GRP94 / HSP82 / HSP90 / HTPG / ADP / GP96 / endoplasmin
Function / homology
Function and homology information


Trafficking and processing of endosomal TLR / Scavenging by Class A Receptors / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Interleukin-4 and Interleukin-13 signaling / Post-translational protein phosphorylation / sarcoplasmic reticulum lumen / : / ATP-dependent protein folding chaperone / unfolded protein binding / melanosome ...Trafficking and processing of endosomal TLR / Scavenging by Class A Receptors / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Interleukin-4 and Interleukin-13 signaling / Post-translational protein phosphorylation / sarcoplasmic reticulum lumen / : / ATP-dependent protein folding chaperone / unfolded protein binding / melanosome / protein folding / perinuclear region of cytoplasm / endoplasmic reticulum / ATP hydrolysis activity / ATP binding
Similarity search - Function
Ribosomal Protein S5; domain 2 - #80 / Endoplasmic reticulum targeting sequence. / Ribosomal Protein S5; domain 2 / 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 ...Ribosomal Protein S5; domain 2 - #80 / Endoplasmic reticulum targeting sequence. / Ribosomal Protein S5; domain 2 / 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 / Histidine kinase-like ATPase, C-terminal domain / Heat Shock Protein 90 / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / Ribosomal protein S5 domain 2-type fold / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Endoplasmin
Similarity search - Component
Biological speciesCanis lupus familiaris (dog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.45 Å
AuthorsDollins, D.E. / Warren, J.J. / Immormino, R.M. / Gewirth, D.T.
CitationJournal: Mol.Cell / Year: 2007
Title: Structures of GRP94-Nucleotide Complexes Reveal Mechanistic Differences between the hsp90 Chaperones.
Authors: Dollins, D.E. / Warren, J.J. / Immormino, R.M. / Gewirth, D.T.
History
DepositionNov 29, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.2Aug 2, 2017Group: Source and taxonomy / Category: entity_src_gen
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Dec 27, 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_struct_conn_angle / struct_conn / struct_ncs_dom_lim / 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 / _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.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.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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE SEQUENCE DATABASE RESIDUES 287-327 WERE DELETED AND REPLACED BY 4 GLYCINES.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Endoplasmin
B: Endoplasmin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,1448
Polymers153,1922
Non-polymers9526
Water4,684260
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5020 Å2
ΔGint-62 kcal/mol
Surface area56960 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)99.080, 108.850, 148.980
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / End auth comp-ID: ILE / End label comp-ID: ILE / Refine code: 6

Dom-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1METMETAA85 - 74934 - 661
2LYSLYSBB87 - 74936 - 661
DetailsDimer in asymmetric unit represents the biological dimer

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Components

#1: Protein Endoplasmin / Heat shock protein 90 kDa beta member 1 / 94 kDa glucose-regulated protein / GRP94


Mass: 76596.016 Da / Num. of mol.: 2 / Fragment: residues 73-754
Mutation: Sequence residues 287-327 were deleted and replaced by four glycines
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Canis lupus familiaris (dog) / Species: Canis lupus / Strain: familiaris / Gene: HSP90B1, TRA1 / Plasmid: pET15b-grp94(73-754d41) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P41148
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 260 / 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: 2.62 Å3/Da / Density % sol: 53.08 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: 26-32% v/v PEG400, 150-225mM MgCl2, and 0.1M Bis-tris propane, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONALS 8.2.110.9795
SYNCHROTRONALS 8.2.120.97950, 0.97960, 0.97180
Detector
TypeIDDetectorDate
ADSC QUANTUM 2101CCDJun 9, 2006
ADSC QUANTUM 2102CCDJun 9, 2006
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SAGITALLY FOCUSED Si(111)SINGLE WAVELENGTHMx-ray1
2SAGITALLY FOCUSED Si(111)MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
20.97961
30.97181
ReflectionResolution: 2.45→50 Å / Num. all: 59883 / Num. obs: 59644 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Rsym value: 0.064 / Net I/σ(I): 15.6
Reflection shellResolution: 2.45→2.5 Å / Redundancy: 4 % / Mean I/σ(I) obs: 2 / Num. unique all: 3474 / Rsym value: 0.758 / % possible all: 97.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQuantumdata collection
XDSdata reduction
XDSdata scaling
SHELXCDphasing
SHELXEmodel building
RefinementMethod to determine structure: MAD / Resolution: 2.45→20 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.899 / SU B: 26.517 / SU ML: 0.308 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.45 / ESU R Free: 0.308 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: The MAD data set was used for phasing, the native data set was used for refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.29947 2970 5 %RANDOM
Rwork0.24756 ---
obs0.25015 56551 99.59 %-
all-59883 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.563 Å2
Baniso -1Baniso -2Baniso -3
1-3.26 Å20 Å20 Å2
2---0.97 Å20 Å2
3----2.29 Å2
Refinement stepCycle: LAST / Resolution: 2.45→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9216 0 58 260 9534
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0229532
X-RAY DIFFRACTIONr_angle_refined_deg1.3561.9712893
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.47451170
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.04124.475438
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.648151762
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.1611556
X-RAY DIFFRACTIONr_chiral_restr0.0940.21451
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.027058
X-RAY DIFFRACTIONr_nbd_refined0.1740.34322
X-RAY DIFFRACTIONr_nbtor_refined0.3110.56582
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2010.5656
X-RAY DIFFRACTIONr_metal_ion_refined0.2970.52
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1560.345
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1990.510
X-RAY DIFFRACTIONr_mcbond_it0.4041.55995
X-RAY DIFFRACTIONr_mcangle_it0.71229348
X-RAY DIFFRACTIONr_scbond_it0.9634079
X-RAY DIFFRACTIONr_scangle_it1.5064.53532
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 4330 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
loose positional0.745
loose thermal210
LS refinement shellResolution: 2.45→2.513 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.377 216 -
Rwork0.331 4014 -
obs--97.92 %
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)
15.9732-0.2363-1.1487.7696-0.0065.3828-0.1256-0.1585-0.80530.69320.06830.09951.2560.35850.05741.10120.4228-0.1320.11290.1801-0.523926.38318.54458.575
22.999-0.7177-0.52239.43483.46968.27490.23270.33950.97990.20150.00330.1763-0.8494-0.0563-0.23610.4611-0.1110.05910.0259-0.0050.0249-22.85843.76859.058
30.8455-0.38590.25611.15560.59110.1479-0.0789-0.16130.0530.70070.1569-0.03750.03060.0309-0.078-0.13350.0564-0.0236-0.3953-0.0377-0.248720.84742.62125.534
40.9015-0.1606-0.48541.09611.037110.49570.0378-0.20920.0820.546-0.0848-0.3156-0.02190.15760.0471-0.2614-0.0341-0.124-0.30630.0867-0.1469-15.81815.88928.387
55.5022.6433-0.02466.4326-0.03854.4451-0.30870.33650.587-0.54290.18580.6635-0.7546-0.66740.1229-0.40470.1244-0.0454-0.04980.12-0.05770.82240.83210.785
66.80282.6778-1.37217.6632-2.54365.9792-0.502-0.0049-1.2111-0.66620.1192-0.82870.79650.82360.3829-0.28850.1470.1568-0.0348-0.02230.21524.88613.536-8.051
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA85 - 34034 - 252
22BB87 - 34036 - 252
33AA341 - 594253 - 506
44BB341 - 594253 - 506
55AA595 - 749507 - 661
66BB595 - 749507 - 661

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