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- PDB-6r4n: Crystal structure of S. cerevisia Niemann-Pick type C protein NPC... -

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Basic information

Entry
Database: PDB / ID: 6r4n
TitleCrystal structure of S. cerevisia Niemann-Pick type C protein NPC2 with ergosterol bound
ComponentsPhosphatidylglycerol/phosphatidylinositol transfer protein
KeywordsLIPID TRANSPORT / Vacuole / Ergosterol
Function / homology
Function and homology information


fungal-type vacuole lumen / intracellular sterol transport / sterol transport / sterol binding / fungal-type vacuole
Similarity search - Function
ML domain, phosphatidylinositol/phosphatidylglycerol transfer protein / GM2-AP, lipid-recognition domain superfamily / Sterol transport protein NPC2-like / ML domain / MD-2-related lipid-recognition domain / Domain involved in innate immunity and lipid metabolism. / Immunoglobulin E-set
Similarity search - Domain/homology
ERGOSTEROL / Phosphatidylglycerol/phosphatidylinositol transfer protein
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / molecular replacement / Resolution: 2.9 Å
AuthorsWinkler, M.B.L. / Kidmose, R.T. / Pedersen, B.P.
Funding support Denmark, 4items
OrganizationGrant numberCountry
European Research Council637372 Denmark
Danish Council for Independent ResearchDFF-4002-0052 Denmark
Other privateCarlsberg Foundation CF17-0180 Denmark
Other privateAIAS fellowship Denmark
CitationJournal: Cell / Year: 2019
Title: Structural Insight into Eukaryotic Sterol Transport through Niemann-Pick Type C Proteins.
Authors: Mikael B L Winkler / Rune T Kidmose / Maria Szomek / Katja Thaysen / Shaun Rawson / Stephen P Muench / Daniel Wüstner / Bjørn Panyella Pedersen /
Abstract: Niemann-Pick type C (NPC) proteins are essential for sterol homeostasis, believed to drive sterol integration into the lysosomal membrane before redistribution to other cellular membranes. Here, ...Niemann-Pick type C (NPC) proteins are essential for sterol homeostasis, believed to drive sterol integration into the lysosomal membrane before redistribution to other cellular membranes. Here, using a combination of crystallography, cryo-electron microscopy, and biochemical and in vivo studies on the Saccharomyces cerevisiae NPC system (NCR1 and NPC2), we present a framework for sterol membrane integration. Sterols are transferred between hydrophobic pockets of vacuolar NPC2 and membrane-protein NCR1. NCR1 has its N-terminal domain (NTD) positioned to deliver a sterol to a tunnel connecting NTD to the luminal membrane leaflet 50 Å away. A sterol is caught inside this tunnel during transport, and a proton-relay network of charged residues in the transmembrane region is linked to this tunnel supporting a proton-driven transport mechanism. We propose a model for sterol integration that clarifies the role of NPC proteins in this essential eukaryotic pathway and that rationalizes mutations in patients with Niemann-Pick disease type C.
History
DepositionMar 22, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 25, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 2, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 16, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.pdbx_formal_charge / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phosphatidylglycerol/phosphatidylinositol transfer protein
B: Phosphatidylglycerol/phosphatidylinositol transfer protein
C: Phosphatidylglycerol/phosphatidylinositol transfer protein
D: Phosphatidylglycerol/phosphatidylinositol transfer protein
E: Phosphatidylglycerol/phosphatidylinositol transfer protein
F: Phosphatidylglycerol/phosphatidylinositol transfer protein
G: Phosphatidylglycerol/phosphatidylinositol transfer protein
H: Phosphatidylglycerol/phosphatidylinositol transfer protein
I: Phosphatidylglycerol/phosphatidylinositol transfer protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)202,03739
Polymers196,3239
Non-polymers5,71430
Water0
1
A: Phosphatidylglycerol/phosphatidylinositol transfer protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,7206
Polymers21,8141
Non-polymers9065
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Phosphatidylglycerol/phosphatidylinositol transfer protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0352
Polymers21,8141
Non-polymers2211
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Phosphatidylglycerol/phosphatidylinositol transfer protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0206
Polymers21,8141
Non-polymers1,2075
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Phosphatidylglycerol/phosphatidylinositol transfer protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0352
Polymers21,8141
Non-polymers2211
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Phosphatidylglycerol/phosphatidylinositol transfer protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5284
Polymers21,8141
Non-polymers7143
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Phosphatidylglycerol/phosphatidylinositol transfer protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4196
Polymers21,8141
Non-polymers6055
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Phosphatidylglycerol/phosphatidylinositol transfer protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,1313
Polymers21,8141
Non-polymers3172
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Phosphatidylglycerol/phosphatidylinositol transfer protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3235
Polymers21,8141
Non-polymers5094
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
I: Phosphatidylglycerol/phosphatidylinositol transfer protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8275
Polymers21,8141
Non-polymers1,0134
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)215.390, 215.390, 129.810
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and resid 33 through 172)
21(chain B and resid 33 through 172)
31(chain C and resid 33 through 172)
41(chain D and resid 33 through 172)
51(chain E and resid 33 through 172)
61(chain F and resid 33 through 172)
71(chain G and resid 33 through 172)
81(chain H and resid 33 through 172)
91(chain I and resid 33 through 172)

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and resid 33 through 172)A33 - 172
211(chain B and resid 33 through 172)B33 - 172
311(chain C and resid 33 through 172)C33 - 172
411(chain D and resid 33 through 172)D33 - 172
511(chain E and resid 33 through 172)E33 - 172
611(chain F and resid 33 through 172)F33 - 172
711(chain G and resid 33 through 172)G33 - 172
811(chain H and resid 33 through 172)H33 - 172
911(chain I and resid 33 through 172)I33 - 172

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Components

#1: Protein
Phosphatidylglycerol/phosphatidylinositol transfer protein / PG/PI-TP / NPC2 homolog


Mass: 21813.635 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: NPC2, YDL046W, D2699 / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): DSY-5 / References: UniProt: Q12408
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 8
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
#4: Chemical
ChemComp-ERG / ERGOSTEROL / Ergosterol


Mass: 396.648 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C28H44O
#5: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: SO4

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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: 5.9 Å3/Da / Density % sol: 79.15 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 4
Details: Lithium Sulfate Monohydrate, Sodium Acetate Trihydrate, PEG 200

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.96864 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 16, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96864 Å / Relative weight: 1
ReflectionResolution: 2.9→47.751 Å / Num. obs: 75858 / % possible obs: 100 % / Redundancy: 11.6 % / Biso Wilson estimate: 65.84 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.326 / Rrim(I) all: 0.341 / Χ2: 0.915 / Net I/σ(I): 8.08
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.9-311.5643.1020.8572800.2793.24699.9
3-3.111.732.191.2663820.4672.2999.9
3.1-3.211.7391.5291.8256040.6551.599100
3.2-3.311.7391.2362.2850040.731.292100
3.3-3.411.6970.9682.9143850.7981.012100
3.4-3.511.6660.7523.7639010.8760.787100
3.5-411.6610.4566.04142100.9520.477100
4-4.211.5520.2769.4539550.9810.289100
4.2-4.511.310.19712.3446840.990.206100
4.5-511.4830.14915.6655010.9940.155100
5-611.730.16214.7562620.9940.169100
6-811.6210.14216.3649850.9950.148100
8-1011.3240.08225.0218030.9980.086100
10-1510.760.06131.0313330.9980.06499.9
15-2010.9220.04639.363340.9990.048100
20-47.7519.770.04538.512350.9990.04892.5

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.9 Å48.06 Å
Translation2.9 Å48.06 Å

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Processing

Software
NameVersionClassification
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
MLPHAREphasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: SIRAS / Resolution: 2.9→47.751 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.87
RfactorNum. reflection% reflection
Rfree0.2567 1990 2.62 %
Rwork0.2258 --
obs0.2266 75826 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 393.7 Å2 / Biso mean: 69.6773 Å2 / Biso min: 11.81 Å2
Refinement stepCycle: final / Resolution: 2.9→47.751 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10121 0 365 0 10486
Biso mean--115.87 --
Num. residues----1296
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01110719
X-RAY DIFFRACTIONf_angle_d1.42314708
X-RAY DIFFRACTIONf_chiral_restr0.091728
X-RAY DIFFRACTIONf_plane_restr0.0111925
X-RAY DIFFRACTIONf_dihedral_angle_d12.1196616
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A6257X-RAY DIFFRACTION12.41TORSIONAL
12B6257X-RAY DIFFRACTION12.41TORSIONAL
13C6257X-RAY DIFFRACTION12.41TORSIONAL
14D6257X-RAY DIFFRACTION12.41TORSIONAL
15E6257X-RAY DIFFRACTION12.41TORSIONAL
16F6257X-RAY DIFFRACTION12.41TORSIONAL
17G6257X-RAY DIFFRACTION12.41TORSIONAL
18H6257X-RAY DIFFRACTION12.41TORSIONAL
19I6257X-RAY DIFFRACTION12.41TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8999-2.97250.38041020.345752565358100
2.9725-3.05280.33512020.324951785380100
3.0528-3.14260.31661020.28353155417100
3.1426-3.2440.30371990.286651985397100
3.244-3.360.3429990.288752945393100
3.36-3.49440.29491020.247253155417100
3.4944-3.65340.2632020.232252045406100
3.6534-3.8460.24711010.228953105411100
3.846-4.08680.24762000.223151855385100
4.0868-4.40220.2511000.200953375437100
4.4022-4.84480.20992020.180852115413100
4.8448-5.54490.2273950.191153445439100
5.5449-6.98250.2408970.222753555452100
6.9825-47.75780.24191870.2045334552199
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)
10.04370.02390.01590.04350.03230.0358-0.00240.0341-0.083-0.0394-0.0248-0.00920.00820.0562-00.11650.04810.01870.1955-0.01470.1767-20.1827-57.5821-0.2349
20.08110.0165-0.00720.02390.04350.02210.0854-0.1027-0.1255-0.1306-0.02790.0301-0.04920.138700.11020.0040.04360.189-0.00170.1687-11.2235-68.244859.8965
30.0641-0.0556-0.0040.0425-0.06260.03930.0585-0.00140.0241-0.0466-0.0874-0.01410.0249-0.0559-00.34260.0354-0.0690.2378-0.02860.2265-36.9157-50.594947.9006
4-0.00180.05460.02510.06950.0048-0.0171-0.11350.087-0.0687-0.0288-0.12430.0520.19010.00280-0.2604-0.6477-0.1423-0.4114-0.36660.2732-51.3485-69.09811.3848
50.0088-0.00830.03560.01560.01580.03240.1934-0.05470.0253-0.06370.193-0.01650.06040.2045-00.36780.0661-0.04310.6392-0.19890.4005-12.5228-61.6258-29.8061
6-0.01110.0365-0.03960.0285-0.01030.00640.1327-0.0682-0.1968-0.2176-0.05050.16890.0413-0.0194-0-0.0267-0.5803-0.1249-0.6722-0.25340.5154-41.6999-82.543356.119
70.0338-0.0062-0.05650.00320.01230.0606-0.0112-0.01960.0182-0.00820.01360.1099-0.0780.049600.18140.03410.01090.1419-0.03070.1566-43.9388-39.054415.1869
80.01830.01510.04470.03220.05790.0578-0.2059-0.0795-0.1126-0.09740.21090.0889-0.08530.08100.3954-0.03230.05580.3569-0.03780.2759-39.2087-63.4812-49.2535
90.0524-0.01990.00240.04570.0490.02530.0802-0.1889-0.0821-0.24390.1350.0649-0.1794-0.045-00.4482-0.0027-0.03090.1736-0.09030.1825-35.5504-38.6749-28.2248
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'B' and resid 33 through 180)B33 - 180
2X-RAY DIFFRACTION2(chain 'H' and resid 29 through 180)H29 - 180
3X-RAY DIFFRACTION3(chain 'G' and resid 31 through 180)G31 - 180
4X-RAY DIFFRACTION4(chain 'A' and resid 31 through 180)A31 - 180
5X-RAY DIFFRACTION5(chain 'D' and resid 31 through 180)D31 - 180
6X-RAY DIFFRACTION6(chain 'I' and resid 31 through 181)I31 - 181
7X-RAY DIFFRACTION7(chain 'C' and resid 31 through 180)C31 - 180
8X-RAY DIFFRACTION8(chain 'E' and resid 32 through 180)E32 - 180
9X-RAY DIFFRACTION9(chain 'F' and resid 31 through 180)F31 - 180

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