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- PDB-5bv7: Crystal structure of human LCAT (L4F, N5D) in complex with Fab of... -

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Basic information

Entry
Database: PDB / ID: 5bv7
TitleCrystal structure of human LCAT (L4F, N5D) in complex with Fab of an agonistic antibody
Components
  • 27C3 heavy chain
  • 27C3 light chain
  • Fab1 heavy chainPIKFYVE
  • Fab1 light chainPIKFYVE
  • Phosphatidylcholine-sterol acyltransferase
KeywordsHYDROLASE/IMMUNE SYSTEM / a/b Hydrolase / Immune system / HYDROLASE-IMMUNE SYSTEM 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 esterase activity / 1-alkyl-2-acetylglycerophosphocholine esterase / apolipoprotein A-I binding / very-low-density lipoprotein particle remodeling / 1-alkyl-2-acetylglycerophosphocholine esterase activity / high-density lipoprotein particle remodeling ...phosphatidylcholine-sterol O-acyltransferase / phosphatidylcholine-sterol O-acyltransferase activity / regulation of high-density lipoprotein particle assembly / platelet-activating factor acetyltransferase activity / sterol esterase activity / 1-alkyl-2-acetylglycerophosphocholine esterase / apolipoprotein A-I binding / very-low-density lipoprotein particle remodeling / 1-alkyl-2-acetylglycerophosphocholine esterase activity / high-density lipoprotein particle remodeling / reverse cholesterol transport / phosphatidylcholine biosynthetic process / lipoprotein biosynthetic process / phosphatidylcholine metabolic process / high-density lipoprotein particle / cholesterol transport / 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Rossmann fold / 3-Layer(aba) Sandwich ...Lecithin:cholesterol/phospholipid:diacylglycerol acyltransferase / Lecithin:cholesterol acyltransferase / Lipases, serine active site. / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Phosphatidylcholine-sterol acyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsPiper, D.E. / Romanow, W.G. / Thibault, S.T. / Walker, N.P.C.
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Agonistic Human Antibodies Binding to Lecithin-Cholesterol Acyltransferase Modulate High Density Lipoprotein Metabolism.
Authors: Gunawardane, R.N. / Fordstrom, P. / Piper, D.E. / Masterman, S. / Siu, S. / Liu, D. / Brown, M. / Lu, M. / Tang, J. / Zhang, R. / Cheng, J. / Gates, A. / Meininger, D. / Chan, J. / Carlson, ...Authors: Gunawardane, R.N. / Fordstrom, P. / Piper, D.E. / Masterman, S. / Siu, S. / Liu, D. / Brown, M. / Lu, M. / Tang, J. / Zhang, R. / Cheng, J. / Gates, A. / Meininger, D. / Chan, J. / Carlson, T. / Walker, N. / Schwarz, M. / Delaney, J. / Zhou, M.
History
DepositionJun 4, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 16, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 23, 2015Group: Data collection / Database references
Revision 1.2Feb 17, 2016Group: Database references
Revision 1.3Aug 22, 2018Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: citation / entity ...citation / entity / entity_src_gen / entity_src_nat / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _entity.src_method / _pdbx_struct_oper_list.symmetry_operation
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...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 / 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 / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_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
Revision 2.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phosphatidylcholine-sterol acyltransferase
L: 27C3 light chain
H: 27C3 heavy chain
B: Fab1 light chain
C: Fab1 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,5228
Polymers143,8455
Non-polymers1,6783
Water6,990388
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11690 Å2
ΔGint-37 kcal/mol
Surface area54330 Å2
2
A: Phosphatidylcholine-sterol acyltransferase
L: 27C3 light chain
H: 27C3 heavy chain
hetero molecules

B: Fab1 light chain
C: Fab1 heavy chain


Theoretical massNumber of molelcules
Total (without water)145,5228
Polymers143,8455
Non-polymers1,6783
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_654-x+3/2,-y,z-1/21
Buried area11430 Å2
ΔGint-25 kcal/mol
Surface area54580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.944, 127.595, 256.079
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Antibody , 4 types, 4 molecules LHBC

#2: Antibody 27C3 light chain


Mass: 22801.076 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#3: Antibody 27C3 heavy chain


Mass: 24696.553 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#4: Antibody Fab1 light chain / PIKFYVE


Mass: 22744.133 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#5: Antibody Fab1 heavy chain / PIKFYVE


Mass: 25644.621 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)

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Protein / Non-polymers , 2 types, 389 molecules A

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


Mass: 47958.465 Da / Num. of mol.: 1 / Mutation: L4F, N5D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Organ (production host): OVARY / Production host: CRICETULUS GRISEUS (Chinese hamster)
References: UniProt: P04180, phosphatidylcholine-sterol O-acyltransferase
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 388 / Source method: isolated from a natural source / Formula: H2O

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Sugars , 2 types, 3 molecules

#6: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1235.105 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpa1-6[DManpa1-3]DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2-2-2-2-2/a4-b1_b4-c1_c3-d1_c6-e1_e3-f1_e6-g1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#7: 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.: 2
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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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.29 Å3/Da / Density % sol: 62.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1 M Hepes pH 7, 5% PEG 20000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 20, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.45→29.88 Å / Num. obs: 66187 / % possible obs: 93.5 % / Redundancy: 5.7 % / Biso Wilson estimate: 44.18 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.048 / Net I/σ(I): 12.2 / Num. measured all: 375174 / Scaling rejects: 16
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.45-2.515.71.2681.62160038190.6120.52185.1
11.75-29.885.50.03434.338366990.9990.01593.7

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Processing

Software
NameVersionClassification
Aimless0.3.6data scaling
PHENIX(phenix.refine: 1.9_1692)refinement
PDB_EXTRACT3.15data extraction
PHASERphasing
MOSFLMdata reduction
Aimless0.3.6data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XWG

4xwg


Resolution: 2.45→29.88 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2415 3224 4.88 %Random selection
Rwork0.1885 62890 --
obs0.1911 66114 93.25 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 121.23 Å2 / Biso mean: 53.133 Å2 / Biso min: 19.27 Å2
Refinement stepCycle: final / Resolution: 2.45→29.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9536 0 111 388 10035
Biso mean--68.25 46.24 -
Num. residues----1241
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.019924
X-RAY DIFFRACTIONf_angle_d1.30613541
X-RAY DIFFRACTIONf_chiral_restr0.0481524
X-RAY DIFFRACTIONf_plane_restr0.0071719
X-RAY DIFFRACTIONf_dihedral_angle_d14.8993542
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 23

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.45-2.48660.31811260.28342447257385
2.4866-2.52540.34971330.27092451258485
2.5254-2.56680.34221260.2722489261587
2.5668-2.6110.35231190.26962563268288
2.611-2.65850.31311350.25862494262987
2.6585-2.70960.32681390.25482565270489
2.7096-2.76480.28881460.24012594274089
2.7648-2.82490.3281340.24492592272691
2.8249-2.89060.27411380.2412664280291
2.8906-2.96280.29261450.23392624276992
2.9628-3.04280.28921410.23522729287092
3.0428-3.13230.26891400.22082672281293
3.1323-3.23330.28661310.22112761289294
3.2333-3.34870.26051390.21142770290995
3.3487-3.48260.26641450.20722791293695
3.4826-3.64080.26611350.19812848298397
3.6408-3.83240.23771350.18122911304699
3.8324-4.07190.22661620.16892889305199
4.0719-4.38540.19631300.15312952308299
4.3854-4.82510.19541600.13612962312299
4.8251-5.51950.20341550.14229593114100
5.5195-6.93960.19821630.1652995315899
6.9396-29.88270.17561470.15323168331599

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