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- PDB-5ksd: Crystal Structure of a Plasma Membrane Proton Pump -

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Basic information

Entry
Database: PDB / ID: 5ksd
TitleCrystal Structure of a Plasma Membrane Proton Pump
ComponentsATPase 2, plasma membrane-type
KeywordsTRANSPORT PROTEIN / P-type ATPase Proton transport
Function / homology
Function and homology information


P-type H+-exporting transporter / proton export across plasma membrane / P-type proton-exporting transporter activity / proton transmembrane transport / regulation of intracellular pH / magnesium ion binding / ATP hydrolysis activity / ATP binding / membrane / plasma membrane
Similarity search - Function
P-type ATPase, subfamily IIIA / Calcium-transporting ATPase, transmembrane domain / Calcium-transporting ATPase, transmembrane domain / Calcium-transporting ATPase, cytoplasmic transduction domain A / Calcium-transporting ATPase, cytoplasmic transduction domain A / Calcium-transporting ATPase, cytoplasmic domain N / Calcium-transporting ATPase, cytoplasmic domain N / Cation transporter/ATPase, N-terminus / Cation-transporting P-type ATPase, N-terminal / Cation transporter/ATPase, N-terminus ...P-type ATPase, subfamily IIIA / Calcium-transporting ATPase, transmembrane domain / Calcium-transporting ATPase, transmembrane domain / Calcium-transporting ATPase, cytoplasmic transduction domain A / Calcium-transporting ATPase, cytoplasmic transduction domain A / Calcium-transporting ATPase, cytoplasmic domain N / Calcium-transporting ATPase, cytoplasmic domain N / Cation transporter/ATPase, N-terminus / Cation-transporting P-type ATPase, N-terminal / Cation transporter/ATPase, N-terminus / E1-E2 ATPase / P-type ATPase, haloacid dehalogenase domain / P-type ATPase, phosphorylation site / P-type ATPase, cytoplasmic domain N / E1-E2 ATPases phosphorylation site. / P-type ATPase, A domain superfamily / P-type ATPase / P-type ATPase, transmembrane domain superfamily / HAD superfamily/HAD-like / haloacid dehalogenase-like hydrolase / HAD superfamily / HAD-like superfamily / Distorted Sandwich / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / : / ATPase 2, plasma membrane-type
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 3.5 Å
AuthorsCroll, T. / Pedersen, B.P. / Nissen, P.
Citation
Journal: Front Physiol / Year: 2017
Title: Improved Model of Proton Pump Crystal Structure Obtained by Interactive Molecular Dynamics Flexible Fitting Expands the Mechanistic Model for Proton Translocation in P-Type ATPases.
Authors: Focht, D. / Croll, T.I. / Pedersen, B.P. / Nissen, P.
#1: Journal: Nature / Year: 2007
Title: Crystal structure of the plasma membrane proton pump.
Authors: Pedersen, B.P. / Buch-Pedersen, M.J. / Morth, J.P. / Palmgren, M.G. / Nissen, P.
History
DepositionJul 8, 2016Deposition site: RCSB / Processing site: PDBE
SupersessionAug 10, 2016ID: 3b8c
Revision 1.0Aug 10, 2016Provider: repository / Type: Initial release
Revision 1.1May 10, 2017Group: Database references
Revision 1.2May 17, 2017Group: Database references
Revision 1.3May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ATPase 2, plasma membrane-type
B: ATPase 2, plasma membrane-type
hetero molecules


Theoretical massNumber of molelcules
Total (without water)184,82512
Polymers182,6182
Non-polymers2,20710
Water00
1
A: ATPase 2, plasma membrane-type
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,4136
Polymers91,3091
Non-polymers1,1045
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ATPase 2, plasma membrane-type
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,4136
Polymers91,3091
Non-polymers1,1045
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.290, 144.420, 312.110
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein ATPase 2, plasma membrane-type / Proton pump 2


Mass: 91309.109 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: AHA2, At4g30190, F9N11.40 / Plasmid: PMP-652 / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): RS-72 / References: UniProt: P19456, EC: 3.6.3.6
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-ACP / PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Comment: AMP-PCP, energy-carrying molecule analogue*YM
#5: Sugar ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM

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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: 4.93 Å3/Da / Density % sol: 75.04 %
Description: Large crystals, often with a growth defect in the center. See Pedersen BP et al Nature 450 (2007) Supplementary Information for details and pictures.
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG 400, Sucrose, KCl, C12E8, Cymal-5, DDM, MES pH 6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.007829 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 3, 2006
RadiationMonochromator: Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.007829 Å / Relative weight: 1
ReflectionResolution: 3.5→100 Å / Num. obs: 49499 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 7.7 % / Biso Wilson estimate: 109.63 Å2 / Rmerge(I) obs: 0.154 / Net I/σ(I): 8.67
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
3.5-3.60.8491.83199.9
3.6-3.70.8382.17199.9
3.7-3.80.8222.361100
3.8-3.90.7522.611100
3.9-40.6942.871100
4-4.30.5553.631100
4.3-4.60.3735.31100
4.6-50.2826.81100
5-60.29.21100
6-70.12815.121100
7-80.08223.631100
8-100.05630.741100
10-120.04533.86199.8
12-150.03834.061100
15-200.03534.2199.8
20-300.03429.89192.3
300.05319.08126.4

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Processing

Software
NameVersionClassification
PHENIXdev_2376refinement
PDB_EXTRACT3.2data extraction
XSCALEdata scaling
autoSHARPphasing
XDSdata reduction
RefinementMethod to determine structure: SIRAS / Resolution: 3.5→52.018 Å / SU ML: 0.68 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 37.36
RfactorNum. reflection% reflectionSelection details
Rfree0.3239 1998 4.04 %random
Rwork0.2873 ---
obs0.2888 49405 99.65 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 323.23 Å2 / Biso mean: 139.6391 Å2 / Biso min: 59.48 Å2
Refinement stepCycle: final / Resolution: 3.5→52.018 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12832 0 138 0 12970
Biso mean--128.49 --
Num. residues----1666
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00313222
X-RAY DIFFRACTIONf_angle_d0.87317928
X-RAY DIFFRACTIONf_chiral_restr0.0482092
X-RAY DIFFRACTIONf_plane_restr0.012248
X-RAY DIFFRACTIONf_dihedral_angle_d17.1917892
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 (%)
3.5001-3.58760.3911390.40843285342498
3.5876-3.68460.41771400.405633393479100
3.6846-3.79290.3971400.376133323472100
3.7929-3.91530.41281430.352233853528100
3.9153-4.05520.36281420.3333593501100
4.0552-4.21750.29661410.309433433484100
4.2175-4.40940.3161410.281733543495100
4.4094-4.64170.29021420.256333643506100
4.6417-4.93230.26471430.260133903533100
4.9323-5.31280.32131430.257133943537100
5.3128-5.84680.33951430.276933863529100
5.8468-6.69130.29161450.276134353580100
6.6913-8.42460.26951470.258434823629100
8.4246-52.02410.32871490.2583559370898
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)
11.65211.5329-1.16851.7824-1.57962.94410.0740.13140.0962-0.32020.67920.61110.3851-1.6194-0.59541.0067-0.04220.15831.66610.03310.9703-16.2064-16.581735.0501
20.5072-1.04190.06082.85-1.41864.0622-0.0345-0.50020.20220.24760.18730.3703-0.8664-0.5776-0.11090.7953-0.04940.01071.3193-0.30580.6883-1.4642-2.567233.6865
32.830.13180.55593.6641.73851.7845-0.10060.8057-0.21030.49450.2419-0.4036-0.72860.5032-0.05591.0701-0.21660.05690.81920.22550.756614.71741.7972-0.4317
4-0.02470.01621.19061.08671.67233.9840.53940.1291-0.73950.8180.1107-0.09772.17090.1719-0.60281.8489-0.0693-0.25391.6781-0.03331.102316.7653-40.158973.9063
53.54750.49081.66380.72740.7824.87990.4434-0.2278-0.13690.0581-0.1759-0.23180.18640.3055-0.44730.8864-0.1325-0.10750.8661-0.08040.569624.9544-21.698675.5427
62.69030.71.02561.8544-0.18940.6825-0.1232-0.96120.0070.89150.21880.2359-0.5339-0.51880.19130.8981-0.9531-0.57110.8658-0.07450.913524.1436-5.7696110.1553
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and (resid 12:479 or resid 1001 or resid 1002 or resid 1003 or resid 1006))A12 - 479
2X-RAY DIFFRACTION1(chain A and (resid 12:479 or resid 1001 or resid 1002 or resid 1003 or resid 1006))A1001
3X-RAY DIFFRACTION1(chain A and (resid 12:479 or resid 1001 or resid 1002 or resid 1003 or resid 1006))A1002
4X-RAY DIFFRACTION1(chain A and (resid 12:479 or resid 1001 or resid 1002 or resid 1003 or resid 1006))A1003
5X-RAY DIFFRACTION1(chain A and (resid 12:479 or resid 1001 or resid 1002 or resid 1003 or resid 1006))A1006
6X-RAY DIFFRACTION2(chain A and (resid 480:703 or resid 1005))A480 - 703
7X-RAY DIFFRACTION2(chain A and (resid 480:703 or resid 1005))A1005
8X-RAY DIFFRACTION3(chain A and (resid 704:844 or resid 1007))A704 - 844
9X-RAY DIFFRACTION3(chain A and (resid 704:844 or resid 1007))A1007
10X-RAY DIFFRACTION4(chain B and (resid 12:479 or resid 1001 or resid 1002 or resid 1003 or resid 1006))B12 - 479
11X-RAY DIFFRACTION4(chain B and (resid 12:479 or resid 1001 or resid 1002 or resid 1003 or resid 1006))B1001
12X-RAY DIFFRACTION4(chain B and (resid 12:479 or resid 1001 or resid 1002 or resid 1003 or resid 1006))B1002
13X-RAY DIFFRACTION4(chain B and (resid 12:479 or resid 1001 or resid 1002 or resid 1003 or resid 1006))B1003
14X-RAY DIFFRACTION4(chain B and (resid 12:479 or resid 1001 or resid 1002 or resid 1003 or resid 1006))B1006
15X-RAY DIFFRACTION5(chain B and (resid 480:703 or resid 1005))B480 - 703
16X-RAY DIFFRACTION5(chain B and (resid 480:703 or resid 1005))B1005
17X-RAY DIFFRACTION6(chain B and (resid 704:844 or resid 1007))B704 - 844
18X-RAY DIFFRACTION6(chain B and (resid 704:844 or resid 1007))B1007

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