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- PDB-5u73: Crystal structure of human Niemann-Pick C1 protein -

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Basic information

Entry
Database: PDB / ID: 5u73
TitleCrystal structure of human Niemann-Pick C1 protein
ComponentsNiemann-Pick C1 protein
KeywordsMEMBRANE PROTEIN
Function / homology
Function and homology information


cyclodextrin metabolic process / cholesterol storage / membrane raft organization / : / intracellular cholesterol transport / intracellular lipid transport / intestinal cholesterol absorption / LDL clearance / programmed cell death / negative regulation of epithelial cell apoptotic process ...cyclodextrin metabolic process / cholesterol storage / membrane raft organization / : / intracellular cholesterol transport / intracellular lipid transport / intestinal cholesterol absorption / LDL clearance / programmed cell death / negative regulation of epithelial cell apoptotic process / cholesterol transport / bile acid metabolic process / establishment of protein localization to membrane / cholesterol efflux / adult walking behavior / lysosomal transport / cholesterol binding / negative regulation of macroautophagy / cellular response to steroid hormone stimulus / protein glycosylation / cellular response to low-density lipoprotein particle stimulus / response to cadmium ion / negative regulation of TORC1 signaling / cholesterol metabolic process / neurogenesis / cholesterol homeostasis / liver development / macroautophagy / autophagy / endocytosis / transmembrane signaling receptor activity / virus receptor activity / signaling receptor activity / nuclear envelope / late endosome membrane / gene expression / lysosome / response to xenobiotic stimulus / symbiont entry into host cell / membrane raft / lysosomal membrane / perinuclear region of cytoplasm / Golgi apparatus / endoplasmic reticulum / extracellular exosome / extracellular region / membrane / plasma membrane
Similarity search - Function
NPC1-like / Niemann-Pick C1, N-terminal / Niemann-Pick C1 N terminus / Sterol-sensing domain of SREBP cleavage-activation / Protein patched/dispatched / Patched family / Sterol-sensing domain (SSD) profile. / Sterol-sensing domain
Similarity search - Domain/homology
NPC intracellular cholesterol transporter 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.348 Å
AuthorsLi, X. / Wang, J. / Blobel, G.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: 3.3 angstrom structure of Niemann-Pick C1 protein reveals insights into the function of the C-terminal luminal domain in cholesterol transport.
Authors: Li, X. / Lu, F. / Trinh, M.N. / Schmiege, P. / Seemann, J. / Wang, J. / Blobel, G.
History
DepositionDec 11, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 27, 2017Provider: repository / Type: Initial release
SupersessionOct 11, 2017ID: 5I31
Revision 1.1Oct 11, 2017Group: Advisory / Structure summary / Category: entity / pdbx_database_PDB_obs_spr / Item: _entity.src_method
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / 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 / pdbx_validate_close_contact / 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.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _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: Niemann-Pick C1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,62212
Polymers142,2551
Non-polymers3,36711
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)181.937, 223.071, 63.208
Angle α, β, γ (deg.)90.00, 105.31, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Niemann-Pick C1 protein


Mass: 142254.859 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NPC1 / Production host: Homo sapiens (human) / References: UniProt: O15118
#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: obtained synthetically
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: Polysaccharide alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 2 / Source method: obtained synthetically
DescriptorTypeProgram
DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#4: 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: obtained synthetically / 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

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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: 4.35 Å3/Da / Density % sol: 71.71 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 5.5
Details: 0.1 M sodium citrate pH 5.5 , 0.1 M NaCl, 12% (vol/vol) PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Aug 30, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.348→50 Å / Num. obs: 17949 / % possible obs: 51.5 % / Redundancy: 3 % / Net I/σ(I): 9.5

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 3.348→41.148 Å / SU ML: 0.51 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 30.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2576 873 4.86 %
Rwork0.2327 --
obs0.234 17949 51.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.348→41.148 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7044 0 218 0 7262
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0047462
X-RAY DIFFRACTIONf_angle_d2.03410198
X-RAY DIFFRACTIONf_dihedral_angle_d15.0344344
X-RAY DIFFRACTIONf_chiral_restr0.0671210
X-RAY DIFFRACTIONf_plane_restr0.0041272
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3484-3.55810.564660.2732232X-RAY DIFFRACTION4
3.5581-3.83260.2658340.235841X-RAY DIFFRACTION15
3.8326-4.2180.24581240.21641999X-RAY DIFFRACTION36
4.218-4.82750.23261610.19213442X-RAY DIFFRACTION62
4.8275-6.0790.26372490.24195034X-RAY DIFFRACTION91
6.079-41.15150.26662990.25785528X-RAY DIFFRACTION99
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)
10.59660.4781-0.12041.24820.22180.74890.1569-0.19340.07880.3177-0.24080.591-0.0289-0.2228-0.00580.37760.02310.14650.30690.00030.322741.632274.354141.4551
22.11780.5972-0.06711.868-0.7692.8431-0.0154-0.2212-0.3297-0.0377-0.21380.1820.1662-0.0020.12460.239-0.02150.18860.1754-0.02750.371146.522888.701336.5322
30.75150.1045-0.28551.415-0.68950.8882-0.2430.2265-0.0177-0.20530.13080.77440.5845-0.38410.07990.6447-0.23070.15170.415-0.12270.577628.90736.927236.7839
41.9865-0.0150.01331.82380.18041.5-0.1215-0.2117-0.3709-0.2475-0.04730.3668-0.0393-0.1977-0.62830.16630.0114-0.00010.07810.03120.057652.572874.727532.9815
50.8101-0.0291-0.80180.9651-0.4830.9874-0.206-0.0125-0.1874-0.24390.14950.1850.174-0.01380.02990.20930.0356-0.09120.19890.01660.075353.172160.461432.2384
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 334 through 508 )
2X-RAY DIFFRACTION2chain 'A' and (resid 509 through 592 )
3X-RAY DIFFRACTION3chain 'A' and (resid 593 through 861 )
4X-RAY DIFFRACTION4chain 'A' and (resid 862 through 908 )
5X-RAY DIFFRACTION5chain 'A' and (resid 909 through 1254 )

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