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- PDB-8vxj: The crystal structure of human apolipoprotein A-I in complex with... -

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Basic information

Entry
Database: PDB / ID: 8vxj
TitleThe crystal structure of human apolipoprotein A-I in complex with Fab 55201
Components
  • Apolipoprotein A-I
  • Fab 55201 heavy chain
  • Fab 55201 light chain
KeywordsLIPID TRANSPORT/IMMUNE SYSTEM / HDL / apolipoprotein / lipid binding / plasma / LIPID TRANSPORT / LIPID TRANSPORT-IMMUNE SYSTEM complex
Function / homology
Function and homology information


Defective ABCA1 causes TGD / high-density lipoprotein particle receptor binding / peptidyl-methionine modification / HDL clearance / spherical high-density lipoprotein particle / Scavenging by Class B Receptors / negative regulation of response to cytokine stimulus / protein oxidation / regulation of intestinal cholesterol absorption / vitamin transport ...Defective ABCA1 causes TGD / high-density lipoprotein particle receptor binding / peptidyl-methionine modification / HDL clearance / spherical high-density lipoprotein particle / Scavenging by Class B Receptors / negative regulation of response to cytokine stimulus / protein oxidation / regulation of intestinal cholesterol absorption / vitamin transport / blood vessel endothelial cell migration / cholesterol import / high-density lipoprotein particle binding / negative regulation of heterotypic cell-cell adhesion / ABC transporters in lipid homeostasis / apolipoprotein A-I receptor binding / apolipoprotein receptor binding / negative regulation of cell adhesion molecule production / negative regulation of cytokine production involved in immune response / HDL assembly / negative regulation of very-low-density lipoprotein particle remodeling / phosphatidylcholine biosynthetic process / glucocorticoid metabolic process / acylglycerol homeostasis / phosphatidylcholine-sterol O-acyltransferase activator activity / positive regulation of phospholipid efflux / Chylomicron remodeling / cellular response to lipoprotein particle stimulus / Chylomicron assembly / high-density lipoprotein particle clearance / phospholipid efflux / chylomicron / high-density lipoprotein particle remodeling / positive regulation of cholesterol metabolic process / lipid storage / reverse cholesterol transport / phospholipid homeostasis / high-density lipoprotein particle assembly / chemorepellent activity / low-density lipoprotein particle / lipoprotein biosynthetic process / cholesterol transfer activity / cholesterol transport / high-density lipoprotein particle / very-low-density lipoprotein particle / endothelial cell proliferation / regulation of Cdc42 protein signal transduction / HDL remodeling / cholesterol efflux / triglyceride homeostasis / Scavenging by Class A Receptors / negative regulation of interleukin-1 beta production / adrenal gland development / negative chemotaxis / cholesterol binding / cholesterol biosynthetic process / positive regulation of Rho protein signal transduction / amyloid-beta formation / positive regulation of cholesterol efflux / endocytic vesicle / negative regulation of tumor necrosis factor-mediated signaling pathway / Scavenging of heme from plasma / Retinoid metabolism and transport / cholesterol metabolic process / positive regulation of stress fiber assembly / heat shock protein binding / endocytic vesicle lumen / positive regulation of substrate adhesion-dependent cell spreading / positive regulation of phagocytosis / cholesterol homeostasis / integrin-mediated signaling pathway / Post-translational protein phosphorylation / Heme signaling / PPARA activates gene expression / phospholipid binding / negative regulation of inflammatory response / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Platelet degranulation / extracellular vesicle / : / amyloid-beta binding / cytoplasmic vesicle / blood microparticle / secretory granule lumen / early endosome / protein stabilization / G protein-coupled receptor signaling pathway / Amyloid fiber formation / receptor ligand activity / endoplasmic reticulum lumen / signaling receptor binding / enzyme binding / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / plasma membrane / cytosol
Similarity search - Function
Apolipoprotein A/E / : / Apolipoprotein A1/A4/E domain
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsTou, H.I. / Metcalfe, R.D. / Khandokar, Y. / Griffin, M.D.W.
Funding support Australia, 2items
OrganizationGrant numberCountry
Australian Research Council (ARC)DP170104046 Australia
Australian Research Council (ARC)FT140100544 Australia
CitationJournal: J.Mol.Biol. / Year: 2025
Title: The structure of the apolipoprotein A-I monomer provides insights into its oligomerisation and lipid-binding mechanisms.
Authors: Tou, H.I. / Rosenes, Z. / Khandokar, Y. / Zlatic, C. / Metcalfe, R. / Mok, Y.F. / Morton, C.J. / Gooley, P.R. / Griffin, M.D.W.
History
DepositionFeb 4, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 27, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Apolipoprotein A-I
H: Fab 55201 heavy chain
L: Fab 55201 light chain
D: Apolipoprotein A-I
A: Fab 55201 heavy chain
B: Fab 55201 light chain


Theoretical massNumber of molelcules
Total (without water)147,6906
Polymers147,6906
Non-polymers00
Water66737
1
C: Apolipoprotein A-I
H: Fab 55201 heavy chain
L: Fab 55201 light chain


Theoretical massNumber of molelcules
Total (without water)73,8453
Polymers73,8453
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Apolipoprotein A-I
A: Fab 55201 heavy chain
B: Fab 55201 light chain


Theoretical massNumber of molelcules
Total (without water)73,8453
Polymers73,8453
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.530, 67.472, 167.123
Angle α, β, γ (deg.)90.000, 95.742, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "A"
d_2ens_1chain "H"
d_1ens_2chain "B"
d_2ens_2chain "L"
d_1ens_3chain "C"
d_2ens_3chain "D"

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_1ens_1GLUGLUASPASPAE1 - 2241 - 224
d_2ens_1GLUGLUASPASPHB1 - 2241 - 224
d_1ens_2ASPASPGLUGLUBF1 - 2121 - 212
d_2ens_2ASPASPGLUGLULC1 - 2121 - 212
d_1ens_3SERSERGLUGLUCA6 - 1836 - 183
d_2ens_3SERSERGLUGLUDD6 - 1836 - 183

NCS ensembles :
ID
ens_1
ens_2
ens_3

NCS oper:
IDCodeMatrixVector
1given(-0.99908812084, -0.0363011995858, -0.022475535679), (-0.0384183904031, 0.994009775173, 0.102316147993), (0.018626703258, 0.103086321934, -0.994497992032)-5.63123431792, -14.6318998765, 136.117228236
2given(-0.997996515901, -0.0599268474507, -0.0202910621821), (-0.0618449684989, 0.99166320524, 0.113045509616), (0.0133474387515, 0.114073924836, -0.993382597769)-5.85649856283, -14.7705534094, 136.507227297
3given(-0.999983888777, -0.00228913225149, 0.0051944259283), (-0.0031488675268, 0.985078444907, -0.172077139716), (-0.00472300968536, -0.172090723902, -0.985069782262)-7.73574303803, 12.474903519, 136.06089943

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Components

#1: Protein Apolipoprotein A-I / Apolipoprotein A-I(1-242)


Mass: 28120.637 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: APOA1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P02647
#2: Antibody Fab 55201 heavy chain


Mass: 23157.350 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)
#3: Antibody Fab 55201 light chain


Mass: 22567.143 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsThe authors state that the sequence of Fab 55201 is unknown. Please see publication for details of ...The authors state that the sequence of Fab 55201 is unknown. Please see publication for details of the sequence assignment process.

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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: 2.22 Å3/Da / Density % sol: 44.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 15% PEG 6000, 0.1 M trisodium citrate-citric acid, pH 5.5, 0.02% NaN3

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 5, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.7→45.6 Å / Num. obs: 35513 / % possible obs: 98.9 % / Redundancy: 6.9 % / Biso Wilson estimate: 76.67 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.145 / Rpim(I) all: 0.09 / Rrim(I) all: 0.171 / Net I/σ(I): 6.7
Reflection shellResolution: 2.7→2.83 Å / Redundancy: 7.2 % / Rmerge(I) obs: 2.358 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 4641 / CC1/2: 0.569 / Rpim(I) all: 1.432 / Rrim(I) all: 2.764 / % possible all: 98.5

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
XDSdata scaling
PHASERphasing
Cootmodel building
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→45.6 Å / SU ML: 0.6348 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 40.2592
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2981 1805 5.1 %
Rwork0.2663 33571 -
obs0.2679 35376 98.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 103.78 Å2
Refinement stepCycle: LAST / Resolution: 2.7→45.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9238 0 0 37 9275
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00149422
X-RAY DIFFRACTIONf_angle_d0.469512796
X-RAY DIFFRACTIONf_chiral_restr0.03741444
X-RAY DIFFRACTIONf_plane_restr0.00321656
X-RAY DIFFRACTIONf_dihedral_angle_d9.19133396
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2EAX-RAY DIFFRACTIONTorsion NCS0.653346877399
ens_2d_2FBX-RAY DIFFRACTIONTorsion NCS0.713570861881
ens_3d_2ACX-RAY DIFFRACTIONTorsion NCS0.87590766485
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.770.53631330.52712541X-RAY DIFFRACTION97.66
2.77-2.850.45781450.46412534X-RAY DIFFRACTION98.42
2.85-2.950.46311520.42272549X-RAY DIFFRACTION97.23
2.95-3.050.46411310.36592566X-RAY DIFFRACTION98.76
3.05-3.170.36331260.33922539X-RAY DIFFRACTION97.98
3.17-3.320.3681420.3232567X-RAY DIFFRACTION97.87
3.32-3.490.3691350.32932571X-RAY DIFFRACTION98.26
3.49-3.710.29161420.27932580X-RAY DIFFRACTION98.48
3.71-40.35361400.26832587X-RAY DIFFRACTION98.8
4-4.40.24311360.23592589X-RAY DIFFRACTION98.73
4.4-5.040.26391450.22262601X-RAY DIFFRACTION98.53
5.04-6.340.2481440.2412634X-RAY DIFFRACTION99
6.35-45.60.23441340.20432713X-RAY DIFFRACTION98.96
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)
10.263228849960.1550259775390.1843552983370.6330759669960.5274714348530.4386873842410.09268185407890.00565985505448-0.2016631163-0.0108505282621-0.03699968605280.056357309015-0.02488869369940.1136152591618.57106710926E-60.958376022165-0.217901056689-0.1417082227441.997729903270.1699730676260.940186357617-10.63766578362.2407838247955.4316322082
21.107423101670.154220037499-0.4024469319810.560050328669-0.3064990685660.7017957230190.0457065044311-0.321968304054-0.02941026693790.143116975045-0.1688602642760.0408924204572-0.1748386157620.295433429819-0.05235673480270.3783352603050.0194421189234-0.01860693582510.04292311434080.01795615477360.514716105803-51.2139357445-4.256847826498.42891978699
30.86602033845-0.08027335720690.5094597269960.00634618756104-0.138517390970.754854478230.000706731861158-0.6907024543820.0284471364586-0.0164250193969-0.132636343840.06716807479190.0947141970014-0.555978525072-0.0105830874050.5979127881280.0216154078663-0.04683985040680.710975860274-0.1672406644480.703698395348-67.3367494541-7.5858671382614.7510659423
40.3067327918990.206814550416-0.06791792232450.158748811617-0.1564551119150.48553083497-0.3213197313290.4047551763280.3148133055560.04037248517730.171115225809-0.0778859441485-0.060285737484-0.2542291064650.0003843268779541.02242245843-0.144008964781-0.205299411441.879039720890.1398185427761.00249731933.185929890565.1775557693781.1201439013
50.0683015613333-0.02862807051990.1010853833310.136187971248-0.2252001799590.341140635034-0.1820053357560.8517580961420.276308281124-0.1999606963850.1180942292690.005317014736220.072000853920.5516406753240.004372774401160.5349224158160.04076568611210.02444048271130.8464550631480.08279403484940.59850657188842.7627359143-1.19472764985129.069456195
60.6407885616750.282723542429-0.3483179479640.3146310723340.3803965731881.4929524003-0.111313073580.7163556837150.395683514428-0.0193584945222-0.170802249032-0.2476131568950.6094056954081.37876354718-0.5013617052410.6058643395280.158236549485-0.08536962904691.510467399510.1988740699430.74637276712559.2880225765-3.08090220741123.011158066
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain 'C' and resid 6 through 183)CA6 - 1831 - 178
22(chain 'H' and resid 1 through 224)HB1 - 2241 - 224
33(chain 'L' and resid 1 through 212)LC1 - 2121 - 212
44(chain 'D' and resid 6 through 183)DD6 - 1831 - 178
55(chain 'A' and resid 1 through 224)AE1 - 2241 - 224
66(chain 'B' and resid 1 through 212)BF1 - 2121 - 212

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