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- PDB-9qqd: cryoEM structure of Bovine Serum Albumin -

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Basic information

Entry
Database: PDB / ID: 9qqd
TitlecryoEM structure of Bovine Serum Albumin
ComponentsAlbumin
KeywordsTRANSPORT PROTEIN / Lipid binding / metal binding / Albumin / disulfide rich / protein binding / METAL BINDING PROTEIN
Function / homology
Function and homology information


cellular response to calcium ion starvation / enterobactin binding / negative regulation of mitochondrial depolarization / toxic substance binding / cellular response to starvation / fatty acid binding / pyridoxal phosphate binding / protein-containing complex / DNA binding / extracellular space ...cellular response to calcium ion starvation / enterobactin binding / negative regulation of mitochondrial depolarization / toxic substance binding / cellular response to starvation / fatty acid binding / pyridoxal phosphate binding / protein-containing complex / DNA binding / extracellular space / extracellular region / metal ion binding / 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 speciesBos taurus (domestic cattle)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsManikandan, K. / Jason, V.R.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Diamond Light Source United Kingdom
Citation
Journal: To Be Published
Title: cryoEM structure of Bovine Serum Albumin
Authors: Manikandan, K. / Jason, V.R.
#1: Journal: J Struct Biol / Year: 2024
Title: The CryoEM structure of human serum albumin in complex with ligands.
Authors: Claudio Catalano / Kyle W Lucier / Dennis To / Skerdi Senko / Nhi L Tran / Ashlyn C Farwell / Sabrina M Silva / Phat V Dip / Nicole Poweleit / Giovanna Scapin /
Abstract: Human serum albumin (HSA) is the most prevalent plasma protein in the human body, accounting for 60 % of the total plasma protein. HSA plays a major pharmacokinetic function, serving as a ...Human serum albumin (HSA) is the most prevalent plasma protein in the human body, accounting for 60 % of the total plasma protein. HSA plays a major pharmacokinetic function, serving as a facilitator in the distribution of endobiotics and xenobiotics within the organism. In this paper we report the cryoEM structures of HSA in the apo form and in complex with two ligands (salicylic acid and teniposide) at a resolution of 3.5, 3.7 and 3.4 Å, respectively. We expand upon previously published work and further demonstrate that sub-4 Å maps of ∼60 kDa proteins can be routinely obtained using a 200 kV microscope, employing standard workflows. Most importantly, these maps allowed for the identification of small molecule ligands, emphasizing the practical applicability of this methodology and providing a starting point for subsequent computational modeling and in silico optimization.
History
DepositionMar 31, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 14, 2025Provider: repository / Type: Initial release
Revision 1.0May 14, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 14, 2025Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0May 14, 2025Data content type: Additional map / Part number: 2 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0May 14, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 14, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 14, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 14, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0May 14, 2025Data content type: Primary map / Data content type: Primary map / Provider: 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


Theoretical massNumber of molelcules
Total (without water)65,7301
Polymers65,7301
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Albumin / BSA


Mass: 65729.984 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: ALB / Production host: Bos taurus (domestic cattle) / References: UniProt: P02769
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: BSA / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: all / Source: NATURAL
Molecular weightValue: 66 kDa/nm / Experimental value: NO
Source (natural)Organism: Bos taurus (domestic cattle)
Buffer solutionpH: 7.4
SpecimenConc.: 4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: sigma A7906
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil R1.2/1.3
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 130000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 40 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
2EPU3.1image acquisition
4CTFFIND4.1CTF correction
7Coot0.9.8model fitting
10cryoSPARC4.6.2final Euler assignment
12cryoSPARC4.6.23D reconstruction
13REFMACmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 315886 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT
Atomic model buildingPDB-ID: 4f5s

4f5s


Pdb chain-ID: A / Accession code: 4f5s / Source name: PDB / Type: experimental model
RefinementResolution: 3.1→107.3 Å / Cor.coef. Fo:Fc: 0.926 / SU B: 10.571 / SU ML: 0.184 / ESU R: 0.357
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflection
Rwork0.32992 --
obs0.32992 56061 100 %
Solvent computationSolvent model: PARAMETERS FOR MASK CACLULATION
Displacement parametersBiso mean: 137.756 Å2
Refinement stepCycle: 1 / Total: 4592
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0060.0124695
ELECTRON MICROSCOPYr_bond_other_d00.0164413
ELECTRON MICROSCOPYr_angle_refined_deg1.7881.8666346
ELECTRON MICROSCOPYr_angle_other_deg0.5941.78710266
ELECTRON MICROSCOPYr_dihedral_angle_1_deg5.8155578
ELECTRON MICROSCOPYr_dihedral_angle_2_deg29.168523
ELECTRON MICROSCOPYr_dihedral_angle_3_deg22.81210864
ELECTRON MICROSCOPYr_dihedral_angle_4_deg
ELECTRON MICROSCOPYr_chiral_restr0.0860.2703
ELECTRON MICROSCOPYr_gen_planes_refined0.0070.025380
ELECTRON MICROSCOPYr_gen_planes_other0.0010.02984
ELECTRON MICROSCOPYr_nbd_refined
ELECTRON MICROSCOPYr_nbd_other
ELECTRON MICROSCOPYr_nbtor_refined
ELECTRON MICROSCOPYr_nbtor_other
ELECTRON MICROSCOPYr_xyhbond_nbd_refined
ELECTRON MICROSCOPYr_xyhbond_nbd_other
ELECTRON MICROSCOPYr_metal_ion_refined
ELECTRON MICROSCOPYr_metal_ion_other
ELECTRON MICROSCOPYr_symmetry_vdw_refined
ELECTRON MICROSCOPYr_symmetry_vdw_other
ELECTRON MICROSCOPYr_symmetry_hbond_refined
ELECTRON MICROSCOPYr_symmetry_hbond_other
ELECTRON MICROSCOPYr_symmetry_metal_ion_refined
ELECTRON MICROSCOPYr_symmetry_metal_ion_other
ELECTRON MICROSCOPYr_mcbond_it8.67613.22315
ELECTRON MICROSCOPYr_mcbond_other8.67613.1992315
ELECTRON MICROSCOPYr_mcangle_it13.53323.6662892
ELECTRON MICROSCOPYr_mcangle_other13.5323.6722893
ELECTRON MICROSCOPYr_scbond_it11.26514.4592380
ELECTRON MICROSCOPYr_scbond_other11.26314.4642381
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other18.71225.9283455
ELECTRON MICROSCOPYr_long_range_B_refined25.79157.9319765
ELECTRON MICROSCOPYr_long_range_B_other25.789157.9419766
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
LS refinement shellResolution: 3.1→3.181 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0 0 -
Rwork1.789 4137 -
obs--100 %

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