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- EMDB-53298: cryoEM structure of Bovine Serum Albumin -

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Basic information

Entry
Database: EMDB / ID: EMD-53298
TitlecryoEM structure of Bovine Serum Albumin
Map dataFinal map from cryoSPARC refinement
Sample
  • Organelle or cellular component: BSA
    • Protein or peptide: Albumin
KeywordsLipid binding / metal binding / Albumin / disulfide rich / protein binding / METAL BINDING PROTEIN / TRANSPORT 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 / extracellular space / DNA binding ...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 / extracellular space / DNA binding / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsManikandan K / Jason VR
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Diamond Light Source United Kingdom
CitationJournal: 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, 2025-
Header (metadata) releaseMay 14, 2025-
Map releaseMay 14, 2025-
UpdateMay 14, 2025-
Current statusMay 14, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53298.png

Downloads & links

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Map

FileDownload / File: emd_53298.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFinal map from cryoSPARC refinement
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 256 pix.
= 236.8 Å		0.93 Å/pix.
x 256 pix.
= 236.8 Å		0.93 Å/pix.
x 256 pix.
= 236.8 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.925 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.29439074 - 0.709802
Average (Standard dev.)-0.000008955158 (±0.01578265)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 236.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_53298_msk_1.map
Projections & Slices
AxesZYX

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Additional map: focused mask refinement map

Fileemd_53298_additional_1.map
Annotationfocused mask refinement map
Projections & Slices
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Histogram

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Additional map: sharpened combined map

Fileemd_53298_additional_2.map
Annotationsharpened combined map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

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Half map: Half map 1

Fileemd_53298_half_map_1.map
AnnotationHalf map 1
Projections & Slices
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Slices (1/2)
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Histogram

Histogram (log scale)

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Half map: Half map 2

Fileemd_53298_half_map_2.map
AnnotationHalf map 2
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Sample components

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Entire : BSA

EntireName: BSA
Components
  • Organelle or cellular component: BSA
    • Protein or peptide: Albumin

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Supramolecule #1: BSA

SupramoleculeName: BSA / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Bos taurus (domestic cattle)
Molecular weightTheoretical: 66 kDa/nm

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Macromolecule #1: Albumin

MacromoleculeName: Albumin / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (domestic cattle)
Molecular weightTheoretical: 65.729984 KDa
Recombinant expressionOrganism: Bos taurus (domestic cattle)
SequenceString: GKSEIAHRFK DLGEEHFKGL VLIAFSQYLQ QCPFDEHVKL VNELTEFAKT CVADESHAGC EKSLHTLFGD ELCKVASLRE TVGDMADCC EKQEPERNEC FLSHKDDSPD LPKLKPDPNT LCDEFKADEK KFWGKYLYEI ARRHPYFYAP ELLYYANKYN G VFQECCQA ...String:
GKSEIAHRFK DLGEEHFKGL VLIAFSQYLQ QCPFDEHVKL VNELTEFAKT CVADESHAGC EKSLHTLFGD ELCKVASLRE TVGDMADCC EKQEPERNEC FLSHKDDSPD LPKLKPDPNT LCDEFKADEK KFWGKYLYEI ARRHPYFYAP ELLYYANKYN G VFQECCQA EDKGACVLPK IETMREKVLV SSARQRLRCA SIQKFGERAL KAWSVARLSQ KFPKAEFVEV TKLVTELTKV HK ECCHGDL LECADDRADL AKYICDNQDT ISSKLKECCD KPLLEKSHCI AEVEKDAVPE NLPPLTADFA EDKDVCKNYQ EAK DAFIGS FLYEYSRRHP EYAVSVLLRL AKEYEATLEE CCAKDDPHAC YSTVFDKLKH LVDEPQNLVK QNCDQFEKLG EYGF QNALV VRYTRKVPQV SSPTLVEVSR SLGKVGTRCC TKPESERMPC TEDYLSLILN RLCVLHEKTP VSEKVTKCCT ESLVN RRPC FSALTPDETY VPKAADEKLF TFHADICTAA DTAKQIKKQT ASVELLKHKP KATEEQLKTV MENFVAFVDK CCAADD KEA CFAVEGPKLV VSTQTA

UniProtKB: Albumin

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration4 mg/mL
BufferpH: 7.4
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300
VitrificationCryogen name: ETHANE
Detailssigma A7906

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: CTFFIND (ver. 4.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: initial model generated from the data
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.6.2) / Number images used: 315886
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC (ver. 4.6.2)

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Atomic model buiding 1

Initial modelPDB ID:

4f5s


Chain - Chain ID: A / Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementProtocol: RIGID BODY FIT
Output model

PDB-9qqd:
cryoEM structure of Bovine Serum Albumin

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