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- PDB-8oi2: Crystal structure of Alb1 megabody in complex with human serum albumin -

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Basic information

Entry
Database: PDB / ID: 8oi2
TitleCrystal structure of Alb1 megabody in complex with human serum albumin
Components
  • Alb1 Megabody
  • Albumin
KeywordsIMMUNE SYSTEM / nanobody / megabody / albumin
Function / homology
Function and homology information


exogenous protein binding / Ciprofloxacin ADME / enterobactin binding / cellular response to calcium ion starvation / Heme biosynthesis / HDL remodeling / negative regulation of mitochondrial depolarization / Prednisone ADME / Heme degradation / Aspirin ADME ...exogenous protein binding / Ciprofloxacin ADME / enterobactin binding / cellular response to calcium ion starvation / 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
Biological speciesHomo sapiens (human)
Helicobacter pylori G27 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsDe Felice, S. / Zoia, G. / Romanyuk, Z. / Pardon, E. / Steyaert, J. / Angelini, A. / Cendron, L.
Funding support Italy, 1items
OrganizationGrant numberCountry
Italian Ministry of Education Italy
CitationJournal: Protein Sci. / Year: 2024
Title: Crystal structure of human serum albumin in complex with megabody reveals unique human and murine cross-reactive binding site.
Authors: De Felice, S. / Romanyuk, Z. / Chinellato, M. / Zoia, G. / Linciano, S. / Kumada, Y. / Pardon, E. / Steyaert, J. / Angelini, A. / Cendron, L.
History
DepositionMar 22, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 3, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Albumin
B: Alb1 Megabody


Theoretical massNumber of molelcules
Total (without water)121,0232
Polymers121,0232
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1100 Å2
ΔGint-7 kcal/mol
Surface area48660 Å2
Unit cell
Length a, b, c (Å)370.359, 73.819, 66.130
Angle α, β, γ (deg.)90.00, 96.90, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Albumin


Mass: 66214.844 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: ALB, GIG20, GIG42, PRO0903, PRO1708, PRO2044, PRO2619, PRO2675, UNQ696/PRO1341
Production host: Komagataella pastoris (fungus) / References: UniProt: P02768
#2: Antibody Alb1 Megabody


Mass: 54808.090 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori G27 (bacteria) / Production host: Escherichia coli (E. coli)

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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: 3.75 Å3/Da / Density % sol: 67 % / Description: rod shape
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8.5
Details: 0.03M Sodium fluoride, 0.03M sodium bromide, 0.03M sodium iodide, 0.1M Tris BICINE pH 8.5, 12% v/v ethylene glycol, 6% w/v PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.8856 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 1, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 3.25→34.27 Å / Num. obs: 43671 / % possible obs: 98.4 % / Redundancy: 3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.044 / Rpim(I) all: 0.044 / Net I/σ(I): 11
Reflection shellResolution: 3.3→3.53 Å / Redundancy: 3 % / Rmerge(I) obs: 0.937 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 4847 / CC1/2: 0.48 / Rpim(I) all: 0.932 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
AutoProcessdata reduction
xia2data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.3→33.86 Å / Cross valid method: THROUGHOUT / σ(F): 1.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2767 2177 4.99 %RANDOM
Rwork0.2255 ---
obs0.2279 43671 83.6 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.3→33.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7680 0 0 0 7680
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003
X-RAY DIFFRACTIONf_angle_d0.609
X-RAY DIFFRACTIONf_dihedral_angle_d4.9391038
X-RAY DIFFRACTIONf_chiral_restr0.0381190
X-RAY DIFFRACTIONf_plane_restr0.0051377
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3-3.370.46351660.40812483X-RAY DIFFRACTION82
3.37-3.450.40911720.39872620X-RAY DIFFRACTION85
3.45-3.540.38261770.36852557X-RAY DIFFRACTION84
3.54-3.630.38081270.33112687X-RAY DIFFRACTION86
3.63-3.740.35721480.28712632X-RAY DIFFRACTION86
3.74-3.860.35891390.26232739X-RAY DIFFRACTION87
3.86-40.24951230.22752666X-RAY DIFFRACTION86
4-4.160.25711220.22522713X-RAY DIFFRACTION86
4.16-4.350.22621380.20652627X-RAY DIFFRACTION85
4.35-4.570.26711490.19352556X-RAY DIFFRACTION83
4.57-4.860.23531110.17932515X-RAY DIFFRACTION81
4.86-5.230.23791180.21012597X-RAY DIFFRACTION82
5.23-5.760.32151230.25342570X-RAY DIFFRACTION83
5.76-6.580.3293910.28362627X-RAY DIFFRACTION83
6.59-8.270.32761440.24122474X-RAY DIFFRACTION80
8.28-33.860.22451290.18022431X-RAY DIFFRACTION79
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)
16.65391.7707-0.45812.20970.54652.47650.36180.9846-0.4573-0.41610.0010.5437-0.242-1.1776-0.47911.23380.2755-0.20851.7163-0.08851.494426.6725-16.24674.0806
23.743-2.35654.40722.9855-4.22617.3762-0.0698-0.39670.01650.2074-0.0777-0.1034-0.2086-0.00740.18991.2322-0.04920.10531.0731-0.16851.168293.4245-23.087952.0314
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resseq 6:583)
2X-RAY DIFFRACTION2(chain B and resseq 1:507)

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