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- EMDB-72282: Human Serum Albumin in complex with four nanobodies: N33, nb139, ... -

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Basic information

Entry
Database: EMDB / ID: EMD-72282
TitleHuman Serum Albumin in complex with four nanobodies: N33, nb139, nb39 & nb104
Map data
Sample
  • Complex: HSA-nb33-nb77-nb125-N42 complex
    • Protein or peptide: Serum albumin
    • Protein or peptide: N33
    • Protein or peptide: nb139
    • Protein or peptide: nb39
    • Protein or peptide: nb104
KeywordsNanobody / VHH / IMMUNE SYSTEM
Function / homology
Function and homology information


bilirubin transport / Ciprofloxacin ADME / exogenous protein binding / cellular response to calcium ion starvation / enterobactin binding / Heme biosynthesis / HDL remodeling / molecular carrier activity / negative regulation of mitochondrial depolarization / Heme degradation ...bilirubin transport / Ciprofloxacin ADME / exogenous protein binding / cellular response to calcium ion starvation / enterobactin binding / Heme biosynthesis / HDL remodeling / molecular carrier activity / negative regulation of mitochondrial depolarization / Heme degradation / Prednisone ADME / Aspirin ADME / antioxidant activity / Scavenging of heme from plasma / toxic substance binding / Recycling of bile acids and salts / platelet alpha granule lumen / fatty acid binding / cellular response to starvation / Post-translational protein phosphorylation / Cytoprotection by HMOX1 / response to nutrient levels / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Platelet degranulation / pyridoxal phosphate binding / protein-folding chaperone binding / blood microparticle / endoplasmic reticulum lumen / copper ion binding / endoplasmic reticulum / Golgi apparatus / protein-containing complex / : / DNA binding / extracellular exosome / extracellular region / identical protein binding / nucleus
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) / Lama glama (llama)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsHang W / Sang Z / Xiang YF / Taylor DJ / Shi Y
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5R01GM154832 United States
CitationJournal: To Be Published
Title: Human Serum Albumin in complex with four nanobodies: N33, nb139, nb39 & nb104
Authors: Sang Z / Huang W / Shi Y
History
DepositionAug 22, 2025-
Header (metadata) releaseMar 25, 2026-
Map releaseMar 25, 2026-
UpdateMar 25, 2026-
Current statusMar 25, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_72282.png

Downloads & links

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Map

FileDownload / File: emd_72282.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.88 Å/pix.
x 400 pix.
= 351.6 Å		0.88 Å/pix.
x 400 pix.
= 351.6 Å		0.88 Å/pix.
x 400 pix.
= 351.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.879 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04
Minimum - Maximum-0.04837825 - 0.1245349
Average (Standard dev.)0.004591237 (±0.0059609585)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 351.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_72282_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_72282_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : HSA-nb33-nb77-nb125-N42 complex

EntireName: HSA-nb33-nb77-nb125-N42 complex
Components
  • Complex: HSA-nb33-nb77-nb125-N42 complex
    • Protein or peptide: Serum albumin
    • Protein or peptide: N33
    • Protein or peptide: nb139
    • Protein or peptide: nb39
    • Protein or peptide: nb104

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Supramolecule #1: HSA-nb33-nb77-nb125-N42 complex

SupramoleculeName: HSA-nb33-nb77-nb125-N42 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Serum albumin

MacromoleculeName: Serum albumin / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 66.571219 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DAHKSEVAHR FKDLGEENFK ALVLIAFAQY LQQCPFEDHV KLVNEVTEFA KTCVADESAE NCDKSLHTLF GDKLCTVATL RETYGEMAD CCAKQEPERN ECFLQHKDDN PNLPRLVRPE VDVMCTAFHD NEETFLKKYL YEIARRHPYF YAPELLFFAK R YKAAFTEC ...String:
DAHKSEVAHR FKDLGEENFK ALVLIAFAQY LQQCPFEDHV KLVNEVTEFA KTCVADESAE NCDKSLHTLF GDKLCTVATL RETYGEMAD CCAKQEPERN ECFLQHKDDN PNLPRLVRPE VDVMCTAFHD NEETFLKKYL YEIARRHPYF YAPELLFFAK R YKAAFTEC CQAADKAACL LPKLDELRDE GKASSAKQRL KCASLQKFGE RAFKAWAVAR LSQRFPKAEF AEVSKLVTDL TK VHTECCH GDLLECADDR ADLAKYICEN QDSISSKLKE CCEKPLLEKS HCIAEVENDE MPADLPSLAA DFVESKDVCK NYA EAKDVF LGMFLYEYAR RHPDYSVVLL LRLAKTYETT LEKCCAAADP HECYAKVFDE FKPLVEEPQN LIKQNCELFE QLGE YKFQN ALLVRYTKKV PQVSTPTLVE VSRNLGKVGS KCCKHPEAKR MPCAEDYLSV VLNQLCVLHE KTPVSDRVTK CCTES LVNR RPCFSALEVD ETYVPKEFNA ETFTFHADIC TLSEKERQIK KQTALVELVK HKPKATKEQL KAVMDDFAAF VEKCCK ADD KETCFAEEGK KLVAASQAAL GL

UniProtKB: Albumin

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Macromolecule #2: N33

MacromoleculeName: N33 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Lama glama (llama)
Molecular weightTheoretical: 14.460989 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
HVQLVESGGG LVQAGGSLRL SCAASDTIDN YARAWFRQAP GKEREFVAAI TWTFGTPYYT DSVKGRFTIS RDDAKNTVYL QMNSLKPED TAVYYCAASL YLPVRTASGG YRLDTDRPQY WGQGTQVTVS SE

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Macromolecule #3: nb139

MacromoleculeName: nb139 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Lama glama (llama)
Molecular weightTheoretical: 13.725168 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
AQVQLVESGG GAVQAGGSLQ LSCRASGRTF SPYVMGWFRQ APGKEREFVG LITWSGGTSY ADSVRGRFTA SRDRVKNTVY LQMNSLKPE DTAVYYCAAA YGAGYYVHER QYDYWGQGTQ VTVSEP

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Macromolecule #4: nb39

MacromoleculeName: nb39 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Lama glama (llama)
Molecular weightTheoretical: 13.773204 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
AHVQLVESGG GLVQAGGSLR VSCAASGREF SNYGMGWFRQ APGKEREFVA TISWNGRITF YADSVKGRFT ISRDNAEKTG YLQMNSLKP EDTALYYCAA ETSGWGSKVV PNYDYWGQGT QVTVSEP

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Macromolecule #5: nb104

MacromoleculeName: nb104 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Lama glama (llama)
Molecular weightTheoretical: 13.40478 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
AEVQLVESGG GLAQAGGSLR LSCAASGRTF SNSCMGWFRQ APGKEREFVA TIRSTGHASY ADSVEGRFTV SRDIAKNTVY LEMNSLKPD DTAVYICGAG VSDYGCYRTS GYNSWGQGTQ VTVSEPK

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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

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 130000

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7.0) / Number images used: 291872
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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