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- PDB-5hci: GPN-loop GTPase Npa3 in complex with GDP -

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Basic information

Entry
Database: PDB / ID: 5hci
TitleGPN-loop GTPase Npa3 in complex with GDP
ComponentsGPN-loop GTPase 1
KeywordsHYDROLASE / GPN-loop GTPase / Chaperone / Assembly / RNA polymerase
Function / homology
Function and homology information


nucleocytoplasmic transport / mitotic sister chromatid cohesion / protein import into nucleus / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / GTPase activity / GTP binding / ATP hydrolysis activity / cytosol / cytoplasm
Similarity search - Function
GPN-loop GTPase 1 / GPN-loop GTPase / Conserved hypothetical ATP binding protein / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / GPN-loop GTPase 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsNiesser, J. / Wagner, F.R. / Kostrewa, D. / Muehlbacher, W. / Cramer, P.
Funding support Germany, 4items
OrganizationGrant numberCountry
German Research FoundationGRK1721 Germany
German Research FoundationSFB860 Germany
European Research CouncilTRANSIT Germany
Volkswagen FoundationVW Vorab Germany
CitationJournal: Mol.Cell.Biol. / Year: 2015
Title: Structure of GPN-Loop GTPase Npa3 and Implications for RNA Polymerase II Assembly.
Authors: Niesser, J. / Wagner, F.R. / Kostrewa, D. / Muhlbacher, W. / Cramer, P.
History
DepositionJan 4, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 20, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 24, 2016Group: Database references
Revision 1.2Sep 14, 2016Group: Derived calculations
Revision 1.3Sep 6, 2017Group: Author supporting evidence / Data collection / Category: diffrn_source / pdbx_audit_support
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_audit_support.funding_organization
Revision 1.4May 8, 2024Group: 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
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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 / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GPN-loop GTPase 1
B: GPN-loop GTPase 1
C: GPN-loop GTPase 1
D: GPN-loop GTPase 1
E: GPN-loop GTPase 1
F: GPN-loop GTPase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,67622
Polymers177,5036
Non-polymers3,17316
Water2,180121
1
F: GPN-loop GTPase 1
hetero molecules

A: GPN-loop GTPase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,1957
Polymers59,1682
Non-polymers1,0275
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_445x-1/2,y-1/2,z1
2
C: GPN-loop GTPase 1
hetero molecules

B: GPN-loop GTPase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,1957
Polymers59,1682
Non-polymers1,0275
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_445x-1/2,-y-1/2,-z1
3
B: GPN-loop GTPase 1
hetero molecules

C: GPN-loop GTPase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,1957
Polymers59,1682
Non-polymers1,0275
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_545x+1/2,-y-1/2,-z1
4
A: GPN-loop GTPase 1
hetero molecules

F: GPN-loop GTPase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,1957
Polymers59,1682
Non-polymers1,0275
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x+1/2,y+1/2,z1
Buried area4340 Å2
ΔGint-59 kcal/mol
Surface area20940 Å2
MethodPISA
5
D: GPN-loop GTPase 1
E: GPN-loop GTPase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,2878
Polymers59,1682
Non-polymers1,1196
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4230 Å2
ΔGint-57 kcal/mol
Surface area21750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.990, 119.180, 347.670
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A and (resseq 2:59 or resseq 73:202 or resseq 218:267 )
21chain B and (resseq 2:59 or resseq 73:202 or resseq 218:267 )
31chain C and (resseq 2:59 or resseq 73:202 or resseq 218:267 )
41chain D and (resseq 2:59 or resseq 73:202 or resseq 218:267 )
51chain E and (resseq 2:59 or resseq 73:202 or resseq 218:267 )
61chain F and (resseq 2:59 or resseq 73:202 or resseq 218:267 )

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERLYSLYSchain A and (resseq 2:59 or resseq 73:202 or resseq 218:267 )AA2 - 591 - 58
12GLYGLYASPASPchain A and (resseq 2:59 or resseq 73:202 or resseq 218:267 )AA73 - 20272 - 201
13VALVALHISHISchain A and (resseq 2:59 or resseq 73:202 or resseq 218:267 )AA218 - 267208 - 257
21SERSERLYSLYSchain B and (resseq 2:59 or resseq 73:202 or resseq 218:267 )BB2 - 591 - 58
22GLYGLYASPASPchain B and (resseq 2:59 or resseq 73:202 or resseq 218:267 )BB73 - 20272 - 201
23VALVALHISHISchain B and (resseq 2:59 or resseq 73:202 or resseq 218:267 )BB218 - 267208 - 257
31SERSERLYSLYSchain C and (resseq 2:59 or resseq 73:202 or resseq 218:267 )CC2 - 591 - 58
32GLYGLYASPASPchain C and (resseq 2:59 or resseq 73:202 or resseq 218:267 )CC73 - 20272 - 201
33VALVALHISHISchain C and (resseq 2:59 or resseq 73:202 or resseq 218:267 )CC218 - 267208 - 257
41SERSERLYSLYSchain D and (resseq 2:59 or resseq 73:202 or resseq 218:267 )DD2 - 591 - 58
42GLYGLYASPASPchain D and (resseq 2:59 or resseq 73:202 or resseq 218:267 )DD73 - 20272 - 201
43VALVALHISHISchain D and (resseq 2:59 or resseq 73:202 or resseq 218:267 )DD218 - 267208 - 257
51SERSERLYSLYSchain E and (resseq 2:59 or resseq 73:202 or resseq 218:267 )EE2 - 591 - 58
52GLYGLYASPASPchain E and (resseq 2:59 or resseq 73:202 or resseq 218:267 )EE73 - 20272 - 201
53VALVALHISHISchain E and (resseq 2:59 or resseq 73:202 or resseq 218:267 )EE218 - 267208 - 257
61SERSERLYSLYSchain F and (resseq 2:59 or resseq 73:202 or resseq 218:267 )FF2 - 591 - 58
62GLYGLYASPASPchain F and (resseq 2:59 or resseq 73:202 or resseq 218:267 )FF73 - 20272 - 201
63VALVALHISHISchain F and (resseq 2:59 or resseq 73:202 or resseq 218:267 )FF218 - 267208 - 257

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Components

#1: Protein
GPN-loop GTPase 1 / Essential PCL1-interacting ATPase 1 / GPN-loop GTPase NPA3 / Nucleolar preribosomal-associated protein 3


Mass: 29583.822 Da / Num. of mol.: 6 / Fragment: 1-264 delta 203-211 / Mutation: 1-264 delta 203-211
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: NPA3, EPA1, GPN1, YJR072C, J1821 / Production host: Escherichia coli (E. coli)
References: UniProt: P47122, Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement
#2: Chemical
ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 121 / 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: 3.18 Å3/Da / Density % sol: 61.31 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 9 mM HEPES (pH 7), 45 mM sodium chloride, 4.5 mM magnesium chloride, 5% (vol/vol) Jeffamine M-600

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.99988 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 31, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99988 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 99343 / % possible obs: 99.7 % / Redundancy: 7.15 % / Rsym value: 0.057 / Net I/σ(I): 20.16
Reflection shellResolution: 2.3→2.36 Å / Mean I/σ(I) obs: 1.88 / Rsym value: 1.269 / % possible all: 99.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
Cootmodel building
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→45.248 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 35.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2755 1987 2 %
Rwork0.2377 97356 -
obs0.2385 99343 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 310.54 Å2 / Biso mean: 82.9906 Å2 / Biso min: 34.76 Å2
Refinement stepCycle: final / Resolution: 2.3→45.248 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12065 0 198 121 12384
Biso mean--74.03 60.08 -
Num. residues----1527
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01112522
X-RAY DIFFRACTIONf_angle_d1.29316966
X-RAY DIFFRACTIONf_chiral_restr0.0521904
X-RAY DIFFRACTIONf_plane_restr0.0052119
X-RAY DIFFRACTIONf_dihedral_angle_d16.6784603
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1878X-RAY DIFFRACTIONPOSITIONAL0.091
12B1878X-RAY DIFFRACTIONPOSITIONAL0.091
13C1878X-RAY DIFFRACTIONPOSITIONAL0.089
14D1878X-RAY DIFFRACTIONPOSITIONAL0.06
15E1874X-RAY DIFFRACTIONPOSITIONAL0.074
16F1878X-RAY DIFFRACTIONPOSITIONAL0.058
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3-2.35750.40971400.368968306970100
2.3575-2.42120.40281410.340369007041100
2.4212-2.49250.39761400.328368987038100
2.4925-2.57290.41041410.30496866700799
2.5729-2.66480.40081400.286168837023100
2.6648-2.77150.31031420.272269547096100
2.7715-2.89760.30921400.264568767016100
2.8976-3.05040.34261410.275669177058100
3.0504-3.24140.30111420.255969567098100
3.2414-3.49160.32431430.25669947137100
3.4916-3.84280.27371420.235269707112100
3.8428-4.39850.24081430.211469827125100
4.3985-5.54010.23451440.200970597203100
5.5401-45.25620.21491480.21277271741999
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)
10.56410.19930.01560.9993-0.33431.1443-0.03190.05420.0560.0009-0.1041-0.1058-0.0036-0.0723-0.00010.4079-0.0530.04830.4434-0.07390.495237.096112.1576-32.4533
20.56190.22290.48410.10140.32952.3653-0.11470.2347-0.0637-0.14050.05190.0709-0.16380.2312-0.00040.43460.0095-0.00120.4266-0.0450.58438.8224-19.6724-5.012
30.7473-0.1428-0.20240.5969-0.23020.72960.0356-0.22890.4283-0.19740.14930.08190.04720.23450.0370.3710.028-0.04530.5653-0.21440.58192.0023-23.6916-7.6187
40.73320.1784-0.09840.3778-0.26350.66290.14020.03090.0148-0.0822-0.0354-0.1118-0.0241-0.1714-00.5980.06930.02820.5477-0.01920.477523.1317-52.9113-50.415
50.7496-0.1093-0.02610.90750.61370.9830.0615-0.01970.1187-0.07420.1621-0.2182-0.03950.10890.00010.4422-0.06160.04260.4525-0.09430.572147.8646-49.1751-28.2743
60.4314-0.1646-0.20530.9030.15550.64290.2060.1060.0836-0.3418-0.3372-0.3204-0.13650.159-0.35340.78170.11260.20860.4732-0.09140.3152-15.3182-32.9712-62.3699
70.49930.15240.38590.35960.18910.1946-0.0214-0.04680.04290.04740.0635-0.256-0.01740.05610.00010.57070.01140.17160.4849-0.02960.527419.0574-19.9412-24.2684
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA2 - 267
2X-RAY DIFFRACTION2chain BB2 - 268
3X-RAY DIFFRACTION3chain CC2 - 267
4X-RAY DIFFRACTION4chain DD2 - 268
5X-RAY DIFFRACTION5chain EE2 - 269
6X-RAY DIFFRACTION6chain FF2 - 268
7X-RAY DIFFRACTION7chain GG1 - 6

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