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- PDB-8rgk: Structure of Human Serum Albumin in complex with Aristolochic Aci... -

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Basic information

Entry
Database: PDB / ID: 8rgk
TitleStructure of Human Serum Albumin in complex with Aristolochic Acid at 1.9 A resolution
ComponentsSerum albumin
KeywordsTRANSPORT PROTEIN / Human Serum Albumin / Aristolochic Acid I / Complex / High Resolution
Function / homology
Function and homology information


exogenous protein binding / Ciprofloxacin ADME / cellular response to calcium ion starvation / enterobactin binding / Heme biosynthesis / HDL remodeling / negative regulation of mitochondrial depolarization / Prednisone ADME / Heme degradation / Aspirin ADME ...exogenous protein binding / Ciprofloxacin ADME / cellular response to calcium ion starvation / enterobactin binding / Heme biosynthesis / HDL remodeling / negative regulation of mitochondrial depolarization / Prednisone ADME / Heme degradation / Aspirin ADME / antioxidant activity / toxic substance binding / Scavenging of heme from plasma / Recycling of bile acids and salts / cellular response to starvation / platelet alpha granule lumen / fatty acid binding / Post-translational protein phosphorylation / Cytoprotection by HMOX1 / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / pyridoxal phosphate binding / Platelet degranulation / protein-folding chaperone binding / blood microparticle / copper ion binding / endoplasmic reticulum lumen / Golgi apparatus / endoplasmic reticulum / protein-containing complex / DNA binding / extracellular space / extracellular exosome / extracellular region / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Serum albumin/Alpha-fetoprotein/Afamin / ALB/AFP/VDB / Serum albumin, N-terminal / Serum albumin, conserved site / Serum albumin-like / Serum albumin family / Albumin domain signature. / Albumin domain profile. / serum albumin
Similarity search - Domain/homology
Chem-GOQ / MYRISTIC ACID / Albumin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsPomyalov, S. / Sidorenko, V.S. / Grollman, A.P. / Shoham, G.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Biol.Chem. / Year: 2024
Title: Structural and mechanistic insights into the transport of aristolochic acids and their active metabolites by human serum albumin.
Authors: Pomyalov, S. / Minetti, C.A. / Remeta, D.P. / Bonala, R. / Johnson, F. / Zaitseva, I. / Iden, C. / Golebiewska, U. / Breslauer, K.J. / Shoham, G. / Sidorenko, V.S. / Grollman, A.P.
History
DepositionDec 13, 2023Deposition site: PDBE / Processing site: PDBE
SupersessionJun 26, 2024ID: 6HSC
Revision 1.0Jun 26, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2024Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serum albumin
B: Serum albumin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,80825
Polymers138,9392
Non-polymers3,86923
Water9,530529
1
A: Serum albumin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,19210
Polymers69,4701
Non-polymers1,7239
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Serum albumin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,61615
Polymers69,4701
Non-polymers2,14614
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)94.397, 37.872, 180.248
Angle α, β, γ (deg.)90.000, 105.124, 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

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Components

#1: Protein Serum albumin


Mass: 69469.695 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P02768
#2: Chemical
ChemComp-MYR / MYRISTIC ACID


Mass: 228.371 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C14H28O2
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-GOQ / 8-methoxy-6-nitro-naphtho[1,2-e][1,3]benzodioxole-5-carboxylic acid


Mass: 341.272 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H11NO7 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 529 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.24 Å3/Da / Density % sol: 45.06 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 34% PEG 3350, 25mM sodium Phosphate pH 7, Aristolochic Acid I.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9798 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 11, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 1.9→47.2 Å / Num. obs: 97365 / % possible obs: 98.8 % / Redundancy: 4.2 % / Biso Wilson estimate: 26.35 Å2 / CC1/2: 0.996 / Net I/σ(I): 10.93
Reflection shellResolution: 1.9→1.968 Å / Num. unique obs: 9562 / CC1/2: 0.796

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→47.2 Å / SU ML: 0.3135 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.1697
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2892 4931 5.07 %
Rwork0.2402 92399 -
obs0.2427 97330 98.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.35 Å2
Refinement stepCycle: LAST / Resolution: 1.9→47.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9127 0 269 529 9925
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00379606
X-RAY DIFFRACTIONf_angle_d0.644312906
X-RAY DIFFRACTIONf_chiral_restr0.03531417
X-RAY DIFFRACTIONf_plane_restr0.00591690
X-RAY DIFFRACTIONf_dihedral_angle_d11.50041447
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.920.39421820.38052992X-RAY DIFFRACTION98.05
1.92-1.940.33991570.34112985X-RAY DIFFRACTION99.02
1.94-1.970.33781530.30383088X-RAY DIFFRACTION98.84
1.97-1.990.34611820.28063071X-RAY DIFFRACTION97.92
1.99-2.020.32381620.28172999X-RAY DIFFRACTION99.62
2.02-2.050.33091500.27163069X-RAY DIFFRACTION99.41
2.05-2.080.33851700.28023042X-RAY DIFFRACTION97.84
2.08-2.110.31271830.27653054X-RAY DIFFRACTION99.02
2.11-2.140.33351630.26453048X-RAY DIFFRACTION99.63
2.14-2.170.30271760.26863029X-RAY DIFFRACTION99.35
2.17-2.210.30251620.26373133X-RAY DIFFRACTION99.31
2.21-2.250.30881790.24383016X-RAY DIFFRACTION98.49
2.25-2.30.32321720.2553022X-RAY DIFFRACTION99.13
2.3-2.340.3321340.24313166X-RAY DIFFRACTION99.28
2.34-2.390.30861540.2423070X-RAY DIFFRACTION99.38
2.39-2.450.31531430.23933045X-RAY DIFFRACTION99.04
2.45-2.510.29891450.253160X-RAY DIFFRACTION99.49
2.51-2.580.30621520.25193042X-RAY DIFFRACTION99.22
2.58-2.650.31781490.25843112X-RAY DIFFRACTION99.15
2.65-2.740.31131500.26753149X-RAY DIFFRACTION99.34
2.74-2.840.3081660.25493050X-RAY DIFFRACTION99.01
2.84-2.950.32151530.25013120X-RAY DIFFRACTION98.85
2.95-3.090.26071890.24773048X-RAY DIFFRACTION98.9
3.09-3.250.31751700.243088X-RAY DIFFRACTION98.94
3.25-3.450.28071610.23743131X-RAY DIFFRACTION98.62
3.45-3.720.27131730.21993068X-RAY DIFFRACTION98.63
3.72-4.090.27691750.21183109X-RAY DIFFRACTION98.32
4.09-4.680.24571770.20053112X-RAY DIFFRACTION97.86
4.68-5.90.25981580.20843145X-RAY DIFFRACTION97.95
5.9-47.20.22941910.2153236X-RAY DIFFRACTION97.03

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