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- PDB-5kwy: Structure of human NPC1 middle lumenal domain bound to NPC2 -

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Basic information

Entry
Database: PDB / ID: 5kwy
TitleStructure of human NPC1 middle lumenal domain bound to NPC2
Components
  • Epididymal secretory protein E1
  • Niemann-Pick C1 protein
KeywordsTRANSPORT PROTEIN / human protein complex / NPC1 / NPC2
Function / homology
Function and homology information


regulation of isoprenoid metabolic process / glycolipid transport / intracellular sterol transport / cyclodextrin metabolic process / cholesterol storage / membrane raft organization / : / intracellular cholesterol transport / intracellular lipid transport / intestinal cholesterol absorption ...regulation of isoprenoid metabolic process / glycolipid transport / intracellular sterol transport / cyclodextrin metabolic process / cholesterol storage / membrane raft organization / : / intracellular cholesterol transport / intracellular lipid transport / intestinal cholesterol absorption / cholesterol transfer activity / LDL clearance / programmed cell death / negative regulation of epithelial cell apoptotic process / phospholipid transport / 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 / lysosomal lumen / cholesterol homeostasis / liver development / macroautophagy / response to virus / autophagy / endocytosis / azurophil granule lumen / 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 / Neutrophil degranulation / perinuclear region of cytoplasm / Golgi apparatus / enzyme binding / endoplasmic reticulum / extracellular space / extracellular exosome / extracellular region / membrane / plasma membrane
Similarity search - Function
Npc2 like, ML domain / Sterol transport protein NPC2-like / Immunoglobulin-like - #770 / NPC1-like / ML domain / MD-2-related lipid-recognition domain / Domain involved in innate immunity and lipid metabolism. / Niemann-Pick C1, N-terminal / Niemann-Pick C1 N terminus / Sterol-sensing domain of SREBP cleavage-activation ...Npc2 like, ML domain / Sterol transport protein NPC2-like / Immunoglobulin-like - #770 / NPC1-like / ML domain / MD-2-related lipid-recognition domain / Domain involved in innate immunity and lipid metabolism. / 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 / Immunoglobulin E-set / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
CHOLEST-5-EN-3-YL HYDROGEN SULFATE / NPC intracellular cholesterol transporter 1 / NPC intracellular cholesterol transporter 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.405 Å
AuthorsLi, X.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Clues to the mechanism of cholesterol transfer from the structure of NPC1 middle lumenal domain bound to NPC2.
Authors: Li, X. / Saha, P. / Li, J. / Blobel, G. / Pfeffer, S.R.
History
DepositionJul 19, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 24, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 7, 2016Group: Database references
Revision 1.2Sep 14, 2016Group: Database references
Revision 1.3Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / citation ...chem_comp / citation / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_oper_list / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _citation.journal_id_CSD / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Oct 4, 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: Niemann-Pick C1 protein
B: Niemann-Pick C1 protein
C: Epididymal secretory protein E1
D: Epididymal secretory protein E1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,61410
Polymers85,7964
Non-polymers1,8186
Water1,892105
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6860 Å2
ΔGint-31 kcal/mol
Surface area33960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.956, 109.686, 154.560
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Niemann-Pick C1 protein


Mass: 28234.248 Da / Num. of mol.: 2 / Fragment: unp residues 374-620
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NPC1 / Cell line (production host): BL21(DE3) / Production host: Bacteria (eubacteria) / References: UniProt: O15118
#2: Protein Epididymal secretory protein E1 / / Human epididymis-specific protein 1 / He1 / Niemann-Pick disease type C2 protein


Mass: 14663.812 Da / Num. of mol.: 2 / Fragment: unp residues 20-151
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NPC2, HE1 / Production host: Homo sapiens (human) / References: UniProt: P61916
#3: 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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4
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-C3S / CHOLEST-5-EN-3-YL HYDROGEN SULFATE / CHOLESTEROL-SULFATE / Cholesterol sulfate


Mass: 466.717 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H46O4S
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 105 / 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: 2.45 Å3/Da / Density % sol: 49.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1M MES pH6.5, 0.1M NaCl, 30% (v/v) PEG400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 14, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 32184 / % possible obs: 97.7 % / Redundancy: 3 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 10.14
Reflection shellResolution: 2.4→2.47 Å / Rmerge(I) obs: 0.594

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5F1B, 1NEP

5f1b

1nep


Resolution: 2.405→44.725 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2494 1631 5.07 %
Rwork0.1939 --
obs0.1967 32141 97.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.405→44.725 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5631 0 120 105 5856
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035934
X-RAY DIFFRACTIONf_angle_d0.6848139
X-RAY DIFFRACTIONf_dihedral_angle_d12.5263565
X-RAY DIFFRACTIONf_chiral_restr0.047918
X-RAY DIFFRACTIONf_plane_restr0.0051045
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4055-2.47630.40671480.30342187X-RAY DIFFRACTION86
2.4763-2.55620.3911500.30362487X-RAY DIFFRACTION97
2.5562-2.64750.31831430.27352551X-RAY DIFFRACTION99
2.6475-2.75350.32271420.2592562X-RAY DIFFRACTION100
2.7535-2.87880.31791130.25682585X-RAY DIFFRACTION100
2.8788-3.03060.31461250.22582576X-RAY DIFFRACTION99
3.0306-3.22040.29971390.23062620X-RAY DIFFRACTION100
3.2204-3.4690.24481290.21232561X-RAY DIFFRACTION99
3.469-3.81790.26221190.1832619X-RAY DIFFRACTION99
3.8179-4.36990.21991260.15642596X-RAY DIFFRACTION98
4.3699-5.50410.19631420.14352570X-RAY DIFFRACTION97
5.5041-44.73280.19011550.16512596X-RAY DIFFRACTION95
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)
10.20670.1799-0.0730.8273-0.44290.18780.29610.09860.07910.0238-0.20810.11030.1899-0.3937-0.00150.2786-0.0456-0.00580.5561-0.13520.4031-30.9405-16.483937.1194
20.69870.05970.3027-0.0205-0.00630.38770.25070.40750.1027-0.0194-0.2951-0.11880.1232-0.2334-00.2788-0.01430.05820.3790.02460.2651-19.5517-16.746932.8231
30.04820.0757-0.04420.1119-0.05840.03110.1427-0.13220.33330.2575-0.0359-0.8196-0.4188-0.185700.53230.09780.05390.32230.07050.4562-36.58038.349542.5371
4-0.0146-0.03860.01530.2269-0.32320.3916-0.1116-0.0770.2326-0.01420.39-0.34220.0216-0.23060.00940.2490.01850.04370.3823-0.05250.3637-24.9348-4.878748.1233
50.3541-0.1871-0.19130.09440.19910.36640.09040.02150.0103-0.0896-0.1082-0.1184-0.08940.1748-00.335-0.05220.0770.22490.03370.3485-11.0436-16.967239.0894
60.2448-0.04190.02990.006-0.19710.4493-0.01270.1096-0.19530.27380.0885-0.03910.1773-0.137600.2941-0.06270.04780.2496-0.02020.3255-21.8051-19.795343.9415
7-0.00220.0088-0.02870.2879-0.23350.1571-0.27240.14330.72420.33980.6333-0.07780.1888-0.39380.13570.35760.12610.07140.4353-0.00680.5242-37.6674-5.256748.6955
80.1065-0.11460.07420.13640.03340.0674-0.30590.0611-0.0433-0.04020.06750.4251-0.5676-0.109-0.00020.37380.13020.01840.5214-0.02880.5603-41.27350.921139.9737
90.13830.1440.06490.08040.11440.0525-0.03430.21910.0344-0.23250.11030.1114-0.5514-0.21020.00010.30310.0042-0.00970.7284-0.03980.4598-36.5075-10.688331.1152
100.096-0.11180.03010.0396-0.0007-0.0125-0.0463-0.02530.3259-0.0706-0.14180.0920.56580.6926-0.00010.59820.08430.1280.5972-0.03830.50247.1287-5.704213.3761
110.69470.4042-0.06260.732-0.14610.87050.02850.10350.17610.0337-0.19950.17580.0843-0.4726-00.311-0.03760.01090.3564-0.04090.2841-18.07993.629421.6858
12-0.06210.01230.06150.10210.0142-0.0541-0.02630.2272-0.10690.37260.0592-0.10920.4552-0.2634-0.00440.3995-0.12740.06690.331-0.06870.2704-13.7025-11.769314.1782
130.57250.0484-0.58210.60670.47451.1649-0.08350.10070.0087-0.03980.0233-0.01940.03120.026600.2954-0.01770.00050.2189-0.00950.2494-9.45183.863520.7347
140.2592-0.05470.76310.7685-0.27672.2317-0.26210.339-0.5341-0.51840.52830.136-0.0619-0.70160.82250.5887-0.40290.02280.5872-0.18480.3846-25.4203-14.17645.9949
150.1202-0.24120.24430.4397-0.49780.6128-0.13730.2949-0.3491-0.04910.3130.0596-0.0785-0.64150.05790.3184-0.2501-0.05890.6755-0.03870.4622-29.9734-3.782610.4258
160.05090.00520.010.09810.07450.09650.4194-0.18170.04750.1453-0.12-0.15880.4017-0.510200.363-0.0652-0.02980.45780.0310.4085-11.07647.765759.7215
170.3627-0.18060.34640.58430.35060.6713-0.0994-0.2764-0.0128-0.0859-0.08480.0034-0.2437-0.7676-0.00110.32980.087-0.01240.5066-0.0070.2529-11.897215.857360.4182
180.31750.18910.06170.09850.06650.0052-0.1373-0.1408-0.07380.2947-0.1739-0.3254-0.526-0.0837-0.1050.54390.1007-0.05660.2777-0.1130.2654-2.20821.351460.4933
190.92510.04040.52530.4060.42480.5598-0.1323-0.41560.06710.11720.0899-0.0227-0.5622-0.660200.47810.1732-0.01460.5174-0.00790.3693-10.629819.730864.7426
200.72470.3164-0.29220.1009-0.05410.2062-0.2376-0.04180.1369-0.0487-0.1813-0.13790.11170.1333-0.00010.39640.0345-0.02980.4018-0.03060.3529-6.87514.759657.0948
210.2106-0.1214-0.19840.26130.04930.1830.04960.63950.1395-0.0303-0.0034-0.34950.3656-0.223900.36820.1130.04030.5172-0.00980.42578.8064-21.605114.1088
220.9271-0.5452-0.02580.30080.19290.8028-0.05350.8848-0.145-0.0964-0.0051-0.00230.1601-0.2281-0.00860.31640.0770.02860.524-0.1470.39158.4419-29.393213.9736
230.7983-0.16730.25850.280.17750.26770.1647-0.1889-0.12170.34150.183-0.38250.77890.29480.28030.40780.1177-0.00030.1561-0.05890.442914.9187-32.52723.5916
240.1679-0.1772-0.11060.13710.06190.1224-0.11680.4947-0.4434-0.25870.0048-0.2910.33430.2665-00.49410.10380.08050.6164-0.10640.497917.5594-29.40288.6791
250.2633-0.2439-0.01260.2582-0.25190.1589-0.19310.4155-0.19250.24060.21430.040.60150.4614-0.00020.41940.05120.03180.4437-0.10270.397311.9614-30.564523.3466
260.78210.21240.39570.04140.05130.19530.2573-0.1330.00290.2882-0.3393-0.1682-0.0002-0.0542-0.03020.24910.09060.05690.14260.01010.43793.8943-29.824821.378
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 400:420 )A400 - 420
2X-RAY DIFFRACTION2( CHAIN A AND RESID 421:452 )A421 - 452
3X-RAY DIFFRACTION3( CHAIN A AND RESID 453:466 )A453 - 466
4X-RAY DIFFRACTION4( CHAIN A AND RESID 467:488 )A467 - 488
5X-RAY DIFFRACTION5( CHAIN A AND RESID 489:526 )A489 - 526
6X-RAY DIFFRACTION6( CHAIN A AND RESID 527:560 )A527 - 560
7X-RAY DIFFRACTION7( CHAIN A AND RESID 561:573 )A561 - 573
8X-RAY DIFFRACTION8( CHAIN A AND RESID 574:593 )A574 - 593
9X-RAY DIFFRACTION9( CHAIN A AND RESID 594:607 )A594 - 607
10X-RAY DIFFRACTION10( CHAIN B AND RESID 378:397 )B378 - 397
11X-RAY DIFFRACTION11( CHAIN B AND RESID 398:452 )B398 - 452
12X-RAY DIFFRACTION12( CHAIN B AND RESID 453:495 )B453 - 495
13X-RAY DIFFRACTION13( CHAIN B AND RESID 496:573 )B496 - 573
14X-RAY DIFFRACTION14( CHAIN B AND RESID 574:592 )B574 - 592
15X-RAY DIFFRACTION15( CHAIN B AND RESID 593:613 )B593 - 613
16X-RAY DIFFRACTION16( CHAIN C AND RESID 20:31 )C20 - 31
17X-RAY DIFFRACTION17( CHAIN C AND RESID 32:78 )C32 - 78
18X-RAY DIFFRACTION18( CHAIN C AND RESID 79:94 )C79 - 94
19X-RAY DIFFRACTION19( CHAIN C AND RESID 95:122 )C95 - 122
20X-RAY DIFFRACTION20( CHAIN C AND RESID 123:152 )C123 - 152
21X-RAY DIFFRACTION21( CHAIN D AND RESID 20:40 )D20 - 40
22X-RAY DIFFRACTION22( CHAIN D AND RESID 41:70 )D41 - 70
23X-RAY DIFFRACTION23( CHAIN D AND RESID 71:94 )D71 - 94
24X-RAY DIFFRACTION24( CHAIN D AND RESID 95:115 )D95 - 115
25X-RAY DIFFRACTION25( CHAIN D AND RESID 116:136 )D116 - 136
26X-RAY DIFFRACTION26( CHAIN D AND RESID 137:151 )D137 - 151

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