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- PDB-6mvd: Crystal structure of Lecithin:cholesterol acyltransferase (LCAT) ... -

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Basic information

Entry
Database: PDB / ID: 6mvd
TitleCrystal structure of Lecithin:cholesterol acyltransferase (LCAT) in complex with isopropyl dodec-11-enylfluorophosphonate (IDFP) and a small molecule activator
ComponentsPhosphatidylcholine-sterol acyltransferase
Keywordstransferase/transferase inhibitor / LCAT / acyltransferase / cholesterol / activator / TRANSFERASE / transferase-transferase inhibitor complex
Function / homology
Function and homology information


phosphatidylcholine-sterol O-acyltransferase / phosphatidylcholine-sterol O-acyltransferase activity / regulation of high-density lipoprotein particle assembly / platelet-activating factor acetyltransferase activity / sterol ester esterase activity / 1-alkyl-2-acetylglycerophosphocholine esterase / apolipoprotein A-I binding / 1-alkyl-2-acetylglycerophosphocholine esterase activity / phosphatidylcholine metabolic process / phosphatidylcholine biosynthetic process ...phosphatidylcholine-sterol O-acyltransferase / phosphatidylcholine-sterol O-acyltransferase activity / regulation of high-density lipoprotein particle assembly / platelet-activating factor acetyltransferase activity / sterol ester esterase activity / 1-alkyl-2-acetylglycerophosphocholine esterase / apolipoprotein A-I binding / 1-alkyl-2-acetylglycerophosphocholine esterase activity / phosphatidylcholine metabolic process / phosphatidylcholine biosynthetic process / very-low-density lipoprotein particle remodeling / high-density lipoprotein particle remodeling / reverse cholesterol transport / lipoprotein biosynthetic process / cholesterol transport / high-density lipoprotein particle / HDL remodeling / phospholipid metabolic process / cholesterol metabolic process / cholesterol homeostasis / lipid metabolic process / extracellular space / extracellular exosome / extracellular region
Similarity search - Function
Lecithin:cholesterol/phospholipid:diacylglycerol acyltransferase / Lecithin:cholesterol acyltransferase / Lipases, serine active site. / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-H94 / propan-2-yl hydrogen (R)-ethylphosphonate / NICKEL (II) ION / Phosphatidylcholine-sterol acyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsManthei, K.A. / Chang, L. / Tesmer, J.J.G.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)HL122416 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)HL131288 United States
CitationJournal: Elife / Year: 2018
Title: Molecular basis for activation of lecithin:cholesterol acyltransferase by a compound that increases HDL cholesterol.
Authors: Manthei, K.A. / Yang, S.M. / Baljinnyam, B. / Chang, L. / Glukhova, A. / Yuan, W. / Freeman, L.A. / Maloney, D.J. / Schwendeman, A. / Remaley, A.T. / Jadhav, A. / Tesmer, J.J.
History
DepositionOct 25, 2018Deposition site: RCSB / Processing site: RCSB
SupersessionDec 5, 2018ID: 6DTJ
Revision 1.0Dec 5, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 12, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_DOI ..._citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_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.pdbx_role / _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_symmetry
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Oct 11, 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: Phosphatidylcholine-sterol acyltransferase
B: Phosphatidylcholine-sterol acyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,37618
Polymers87,3812
Non-polymers2,99416
Water36020
1
A: Phosphatidylcholine-sterol acyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,42411
Polymers43,6911
Non-polymers1,73310
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Phosphatidylcholine-sterol acyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9527
Polymers43,6911
Non-polymers1,2616
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)134.697, 106.377, 117.823
Angle α, β, γ (deg.)90.00, 125.45, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein / Sugars , 2 types, 7 molecules AB

#1: Protein Phosphatidylcholine-sterol acyltransferase / Lecithin-cholesterol acyltransferase / Phospholipid-cholesterol acyltransferase


Mass: 43690.727 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LCAT / Production host: Homo sapiens (human)
References: UniProt: P04180, phosphatidylcholine-sterol O-acyltransferase
#2: 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.: 5
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

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Non-polymers , 5 types, 31 molecules

#3: Chemical ChemComp-H9A / propan-2-yl hydrogen (R)-ethylphosphonate


Mass: 152.129 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H13O3P
#4: Chemical ChemComp-H94 / 6-{4-[(4R)-4-hydroxy-6-oxo-4-(trifluoromethyl)-4,5,6,7-tetrahydro-2H-pyrazolo[3,4-b]pyridin-3-yl]piperidin-1-yl}-4-(trifluoromethyl)pyridine-3-carbonitrile


Mass: 474.360 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H16F6N6O2
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 3.93 Å3/Da / Density % sol: 68.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.25 M lithium sulfate, 0.1 M Tris pH 8.5, and 16% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 29, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 3.1→30 Å / Num. obs: 24440 / % possible obs: 98.9 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.115 / Net I/σ(I): 11.1
Reflection shellResolution: 3.1→3.15 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 1.27 / Num. unique obs: 1235 / CC1/2: 0.55 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5TXF

5txf


Resolution: 3.1→28.8 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.907 / SU B: 43.267 / SU ML: 0.341 / Cross valid method: THROUGHOUT / ESU R Free: 0.435 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23932 1145 5.3 %RANDOM
Rwork0.19252 ---
obs0.19508 20413 87.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 70.341 Å2
Baniso -1Baniso -2Baniso -3
1--0.42 Å20 Å2-0.23 Å2
2--1.1 Å20 Å2
3----0.18 Å2
Refinement stepCycle: 1 / Resolution: 3.1→28.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5978 0 183 20 6181
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0146358
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175501
X-RAY DIFFRACTIONr_angle_refined_deg1.3311.6928705
X-RAY DIFFRACTIONr_angle_other_deg0.8221.64912869
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2155740
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.73521.763329
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.68615948
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0871538
X-RAY DIFFRACTIONr_chiral_restr0.0560.2786
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.027046
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021252
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.2465.8952972
X-RAY DIFFRACTIONr_mcbond_other2.2465.8952971
X-RAY DIFFRACTIONr_mcangle_it3.7848.8353708
X-RAY DIFFRACTIONr_mcangle_other3.7838.8353709
X-RAY DIFFRACTIONr_scbond_it2.1376.1463386
X-RAY DIFFRACTIONr_scbond_other2.1316.1363376
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.6649.1214979
X-RAY DIFFRACTIONr_long_range_B_refined6.29470.9267334
X-RAY DIFFRACTIONr_long_range_B_other6.29270.9397333
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.1→3.18 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.423 57 -
Rwork0.312 944 -
obs--55.21 %
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)
10.7527-0.2195-0.14830.34260.38240.47070.0256-0.0269-0.0697-0.0026-0.07220.054-0.0221-0.02270.04660.073-0.01570.04870.19590.0210.0543112.5353-2.4908114.6773
22.2058-1.0640.87580.6833-0.50830.46560.18020.0592-0.0109-0.0476-0.1340.00310.0056-0.0329-0.04620.05860.04720.01930.20070.04620.014277.961721.1487121.3825
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A21 - 505
2X-RAY DIFFRACTION2B21 - 501

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