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- PDB-8y9u: Crystal structure of nanobody MY6323 bound to human serum albumin... -

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Basic information

Entry
Database: PDB / ID: 8y9u
TitleCrystal structure of nanobody MY6323 bound to human serum albumin (HSA)
Components
  • Albumin
  • nanobody MY6323
KeywordsPROTEIN BINDING / antibody
Function / homology
Function and homology information


Ciprofloxacin ADME / exogenous protein binding / cellular response to calcium ion starvation / enterobactin binding / Heme biosynthesis / HDL remodeling / negative regulation of mitochondrial depolarization / Prednisone ADME / Heme degradation / Aspirin ADME ...Ciprofloxacin ADME / exogenous protein binding / 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 / platelet alpha granule lumen / cellular response to starvation / 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 / endoplasmic reticulum / Golgi apparatus / 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)
Vicugna pacos (alpaca)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsDing, Y. / Zhong, P.Y.
Funding support China, 3items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)32070939 China
National Science Foundation (NSF, China)82030106 China
Ministry of Science and Technology (MoST, China)2021YFA0805200 China
CitationJournal: To Be Published
Title: Crystal structure of nanobody MY6323 bound to human serum albumin (HSA)
Authors: Ding, Y. / Zhong, P.Y.
History
DepositionFeb 7, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 12, 2025Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2025Group: Derived calculations / Category: pdbx_struct_assembly / pdbx_struct_assembly_gen

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Albumin
B: nanobody MY6323
C: Albumin
D: nanobody MY6323


Theoretical massNumber of molelcules
Total (without water)162,6114
Polymers162,6114
Non-polymers00
Water00
1
A: Albumin
B: nanobody MY6323


Theoretical massNumber of molelcules
Total (without water)81,3062
Polymers81,3062
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Albumin
D: nanobody MY6323


Theoretical massNumber of molelcules
Total (without water)81,3062
Polymers81,3062
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.420, 65.892, 118.713
Angle α, β, γ (deg.)104.85, 103.41, 91.73
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Albumin / HSA


Mass: 67346.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ALB / Production host: Oryza sativa (Asian cultivated rice) / References: UniProt: P02768
#2: Antibody nanobody MY6323


Mass: 13959.404 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Saccharomyces cerevisiae (brewer's yeast)
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: 2.68 Å3/Da / Density % sol: 54.02 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Ammonium sulfate, 0.1 M Tris pH 8.5, 23% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.979183 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 6, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979183 Å / Relative weight: 1
ReflectionResolution: 3.1→63.4 Å / Num. obs: 29492 / % possible obs: 96.1 % / Redundancy: 3.4 % / CC1/2: 0.996 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.05 / Rrim(I) all: 0.093 / Χ2: 0.92 / Net I/σ(I): 9.6 / Num. measured all: 100447
Reflection shellResolution: 3.1→3.26 Å / % possible obs: 97.9 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.479 / Num. measured all: 15313 / Num. unique obs: 4404 / CC1/2: 0.825 / Rpim(I) all: 0.301 / Rrim(I) all: 0.568 / Χ2: 0.72 / Net I/σ(I) obs: 2.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
Aimless0.7.7data scaling
XDS0.7.7data reduction
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→63.4 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflection
Rfree0.3162 1449 -
Rwork0.2733 --
obs-29473 95.93 %
Refinement stepCycle: LAST / Resolution: 3.1→63.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11064 0 0 0 11064
LS refinement shellResolution: 3.097→3.208 Å
RfactorNum. reflection% reflection
Rfree0.4118 --
Rwork0.3597 --
obs-2996 97.49 %

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