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- PDB-6lkn: Crystal structure of ATP11C-CDC50A in PtdSer-bound E2P state -

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Basic information

Entry
Database: PDB / ID: 6lkn
TitleCrystal structure of ATP11C-CDC50A in PtdSer-bound E2P state
Components
  • Cell cycle control protein 50A
  • Phospholipid-transporting ATPase IG
KeywordsMEMBRANE PROTEIN / P-type ATPase / flippase / apoptosis / phosphatidylserine
Function / homology
Function and homology information


positive regulation of phospholipid translocation / aminophospholipid flippase activity / aminophospholipid transport / phosphatidylserine flippase activity / protein localization to endosome / phospholipid-translocating ATPase complex / ATPase-coupled intramembrane lipid transporter activity / phosphatidylserine floppase activity / positive regulation of protein exit from endoplasmic reticulum / xenobiotic transmembrane transport ...positive regulation of phospholipid translocation / aminophospholipid flippase activity / aminophospholipid transport / phosphatidylserine flippase activity / protein localization to endosome / phospholipid-translocating ATPase complex / ATPase-coupled intramembrane lipid transporter activity / phosphatidylserine floppase activity / positive regulation of protein exit from endoplasmic reticulum / xenobiotic transmembrane transport / phosphatidylethanolamine flippase activity / P-type phospholipid transporter / phospholipid translocation / transport vesicle membrane / azurophil granule membrane / Ion transport by P-type ATPases / specific granule membrane / monoatomic ion transmembrane transport / recycling endosome / positive regulation of neuron projection development / recycling endosome membrane / late endosome membrane / early endosome membrane / apical plasma membrane / lysosomal membrane / Neutrophil degranulation / endoplasmic reticulum membrane / structural molecule activity / Golgi apparatus / magnesium ion binding / endoplasmic reticulum / ATP hydrolysis activity / ATP binding / membrane / plasma membrane
Similarity search - Function
CDC50/LEM3 family / LEM3 (ligand-effect modulator 3) family / CDC50 family / P-type ATPase, subfamily IV / P-type ATPase, C-terminal / P-type ATPase, N-terminal / Phospholipid-translocating ATPase N-terminal / Phospholipid-translocating P-type ATPase C-terminal / Cation transport ATPase (P-type) / E1-E2 ATPase / P-type ATPase, haloacid dehalogenase domain ...CDC50/LEM3 family / LEM3 (ligand-effect modulator 3) family / CDC50 family / P-type ATPase, subfamily IV / P-type ATPase, C-terminal / P-type ATPase, N-terminal / Phospholipid-translocating ATPase N-terminal / Phospholipid-translocating P-type ATPase C-terminal / Cation transport ATPase (P-type) / 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 superfamily
Similarity search - Domain/homology
1-deoxy-alpha-D-mannopyranose / Chem-P5S / Phospholipid-transporting ATPase IG / Cell cycle control protein 50A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.9 Å
AuthorsAbe, K. / Irie, K. / Nakanishi, H. / Hasegawa, K.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Science and TechnologyJPMJCR14M4 Japan
Japan Society for the Promotion of Science (JSPS)17H03653 Japan
CitationJournal: J.Biol.Chem. / Year: 2020
Title: Crystal structure of a human plasma membrane phospholipid flippase.
Authors: Nakanishi, H. / Irie, K. / Segawa, K. / Hasegawa, K. / Fujiyoshi, Y. / Nagata, S. / Abe, K.
History
DepositionDec 19, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 10, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 17, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jul 15, 2020Group: Structure summary / Category: audit_author
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Aug 5, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.5Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phospholipid-transporting ATPase IG
C: Cell cycle control protein 50A
E: Phospholipid-transporting ATPase IG
F: Cell cycle control protein 50A
I: Phospholipid-transporting ATPase IG
J: Cell cycle control protein 50A
M: Phospholipid-transporting ATPase IG
N: Cell cycle control protein 50A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)692,04339
Polymers682,2058
Non-polymers9,83831
Water1448
1
A: Phospholipid-transporting ATPase IG
C: Cell cycle control protein 50A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,20910
Polymers170,5512
Non-polymers2,6578
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9850 Å2
ΔGint-48 kcal/mol
Surface area66690 Å2
MethodPISA
2
E: Phospholipid-transporting ATPase IG
F: Cell cycle control protein 50A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,20910
Polymers170,5512
Non-polymers2,6578
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8610 Å2
ΔGint-42 kcal/mol
Surface area68800 Å2
MethodPISA
3
I: Phospholipid-transporting ATPase IG
J: Cell cycle control protein 50A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,20910
Polymers170,5512
Non-polymers2,6578
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8760 Å2
ΔGint-40 kcal/mol
Surface area70310 Å2
MethodPISA
4
M: Phospholipid-transporting ATPase IG
N: Cell cycle control protein 50A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)172,4179
Polymers170,5512
Non-polymers1,8657
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8670 Å2
ΔGint-36 kcal/mol
Surface area69530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.460, 232.830, 492.890
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 2 types, 8 molecules AEIMCFJN

#1: Protein
Phospholipid-transporting ATPase IG / ATPase IQ / ATPase class VI type 11C / P4-ATPase flippase complex alpha subunit ATP11C


Mass: 129710.633 Da / Num. of mol.: 4 / Mutation: C111W
Source method: isolated from a genetically manipulated source
Details: Amino acid 410 in PDB is BFD, which is BeF-bound Asp.
Source: (gene. exp.) Homo sapiens (human) / Gene: ATP11C, ATPIG, ATPIQ / Cell line (production host): Expi293 / Production host: Homo sapiens (human)
References: UniProt: Q8NB49, P-type phospholipid transporter
#2: Protein
Cell cycle control protein 50A / P4-ATPase flippase complex beta subunit TMEM30A / Transmembrane protein 30A


Mass: 40840.684 Da / Num. of mol.: 4 / Mutation: N190Q, S292W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TMEM30A, C6orf67, CDC50A / Cell line (production host): Expi293 / Production host: Homo sapiens (human) / References: UniProt: Q9NV96

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Sugars , 2 types, 20 molecules

#5: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 16
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#6: Sugar
ChemComp-AH2 / 1-deoxy-alpha-D-mannopyranose / 1,5-Anhydromannitol / 1-deoxy-alpha-D-mannose / 1-deoxy-D-mannose / 1-deoxy-mannose


Type: D-saccharide / Mass: 164.156 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C6H12O5

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Non-polymers , 3 types, 19 molecules

#3: Chemical
ChemComp-P5S / O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine / phosphatidyl serine


Mass: 792.075 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C42H82NO10P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 4.23 Å3/Da / Density % sol: 70.9 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 14-15% PEG4000, 10% glycerol, 5 mM beta-mercaptoethanol, 0.4 M MgSO4

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Data collection

DiffractionMean temperature: 80 K / Ambient temp details: LN2 / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.9→50 Å / Num. obs: 106458 / % possible obs: 71.32 % / Redundancy: 776.9 % / Biso Wilson estimate: 98.24 Å2 / CC1/2: 0.92 / Rmerge(I) obs: 1.141 / Rpim(I) all: 0.0419 / Net I/σ(I): 15.88
Reflection shellResolution: 3.9→4 Å / Redundancy: 698.5 % / Num. unique obs: 1223 / CC1/2: 0.864 / % possible all: 11.64

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PHENIX1.13_2998model building
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6k7l

6k7l


Resolution: 3.9→49.97 Å / SU ML: 0.6547 / Cross valid method: FREE R-VALUE / σ(F): 2.07 / Phase error: 38.7776
Details: Diffractions were strongly anisorlopic. We merged 1588 crystal data to improve data quality.
RfactorNum. reflection% reflection
Rfree0.3501 3779 4.97 %
Rwork0.2812 --
obs0.2846 75980 71.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 161.97 Å2
Refinement stepCycle: LAST / Resolution: 3.9→49.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms44860 0 396 0 45256
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006246317
X-RAY DIFFRACTIONf_angle_d1.193362780
X-RAY DIFFRACTIONf_chiral_restr0.09257060
X-RAY DIFFRACTIONf_plane_restr0.008213433
X-RAY DIFFRACTIONf_dihedral_angle_d20.519517016
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.9-3.950.2403130.2711331X-RAY DIFFRACTION8.97
3.95-40.3227250.2699438X-RAY DIFFRACTION11.9
4-4.060.3399270.2849578X-RAY DIFFRACTION15.66
4.06-4.110.3265380.2884706X-RAY DIFFRACTION19.36
4.11-4.180.3763560.3048858X-RAY DIFFRACTION23.2
4.18-4.240.328610.28181072X-RAY DIFFRACTION29.22
4.24-4.310.3483780.28351289X-RAY DIFFRACTION35.12
4.31-4.380.3224960.30041626X-RAY DIFFRACTION43.72
4.38-4.460.32331040.28181992X-RAY DIFFRACTION54.16
4.46-4.550.30861250.28022283X-RAY DIFFRACTION61.33
4.55-4.640.3511140.28182559X-RAY DIFFRACTION69.19
4.64-4.740.32431650.26022815X-RAY DIFFRACTION75.75
4.74-4.850.31961820.25583049X-RAY DIFFRACTION82.93
4.85-4.980.33041640.26423359X-RAY DIFFRACTION89.67
4.98-5.110.33551730.26413635X-RAY DIFFRACTION97.47
5.11-5.260.33441850.26863741X-RAY DIFFRACTION100
5.26-5.430.32622100.27983716X-RAY DIFFRACTION100
5.43-5.620.35052090.29243745X-RAY DIFFRACTION100
5.62-5.850.36451830.29893758X-RAY DIFFRACTION100
5.85-6.110.36042090.30973721X-RAY DIFFRACTION100
6.11-6.440.41251890.3093771X-RAY DIFFRACTION100
6.44-6.840.37312050.30823797X-RAY DIFFRACTION100
6.84-7.360.39221890.30563757X-RAY DIFFRACTION100
7.36-8.10.34951790.28563824X-RAY DIFFRACTION100
8.1-9.270.33512030.2613851X-RAY DIFFRACTION100
9.27-11.650.32351820.22463878X-RAY DIFFRACTION99.95
11.65-49.970.38572150.31684052X-RAY DIFFRACTION99.81
Refinement TLS params.Method: refined / Origin x: -25.8822080037 Å / Origin y: 100.493022409 Å / Origin z: -125.137573873 Å
111213212223313233
T0.797171610322 Å2-0.0309929675227 Å2-0.10846172831 Å2-1.13073480541 Å20.223457821918 Å2--0.628623400895 Å2
L-0.281939005254 °2-0.249028377706 °20.00503248075528 °2-0.285809985355 °2-0.931920259273 °2---0.716252988762 °2
S0.300909823979 Å °-0.0124069657742 Å °-0.0103155924219 Å °-0.393918453054 Å °-0.136255698254 Å °-0.176163060786 Å °-0.0820420517088 Å °0.0999485834153 Å °-0.0315345514706 Å °
Refinement TLS groupSelection details: all

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