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- PDB-8z8v: Crystal structure of human serum albumin in complex with ALB8(VHH... -

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Basic information

Entry
Database: PDB / ID: 8z8v
TitleCrystal structure of human serum albumin in complex with ALB8(VHH) domain of ozoralizumab
Components
  • ALB8:VHH
  • Serum albumin
KeywordsTRANSPORT PROTEIN / HSA / VHH / Ozoralizumab
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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsMima, M. / Mishima-Tsumagari, C.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2024
Title: Structural design of the anti-TNF alpha therapeutic NANOBODY® compound, ozoralizumab, to support its potent and sustained clinical efficacy.
Authors: Mima, M. / Mishima-Tsumagari, C. / Nakano, K. / Morimoto, M. / Ogata, H. / Sakata, M. / Iwaoka, R. / Iwata, K. / Hachiuma, K. / Iwamoto, K. / Fujii, Y. / Kurokawa, T.
History
DepositionApr 22, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 4, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serum albumin
B: ALB8:VHH


Theoretical massNumber of molelcules
Total (without water)79,7112
Polymers79,7112
Non-polymers00
Water2,288127
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.290, 60.900, 62.810
Angle α, β, γ (deg.)89.51, 63.72, 76.49
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Serum albumin


Mass: 66571.219 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P02768
#2: Antibody ALB8:VHH


Mass: 13139.515 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 127 / Source method: isolated from a natural source / Formula: H2O
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: 2.51 Å3/Da / Density % sol: 50.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 4.7 / Details: 100 mM SPG Buffer (pH4.7) 21 % PEG1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 29, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.05→45.3 Å / Num. obs: 47566 / % possible obs: 97.6 % / Redundancy: 3.9 % / CC1/2: 0.994 / Net I/σ(I): 7.09
Reflection shellResolution: 2.05→2.17 Å / Num. unique obs: 7440 / CC1/2: 0.554

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→45.3 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.942 / SU B: 7.32 / SU ML: 0.18 / Cross valid method: THROUGHOUT / ESU R: 0.208 / ESU R Free: 0.175 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23854 2399 5 %RANDOM
Rwork0.20242 ---
obs0.20432 45167 97.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.08 Å2
Baniso -1Baniso -2Baniso -3
1--0.8 Å2-2.21 Å21.81 Å2
2--1.69 Å20.41 Å2
3----0.29 Å2
Refinement stepCycle: 1 / Resolution: 2.05→45.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5403 0 0 127 5530
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0135522
X-RAY DIFFRACTIONr_bond_other_d0.0010.0155204
X-RAY DIFFRACTIONr_angle_refined_deg1.5181.6487462
X-RAY DIFFRACTIONr_angle_other_deg1.3131.58312065
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2385685
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.42823.214280
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.53915998
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.721529
X-RAY DIFFRACTIONr_chiral_restr0.0790.2709
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026190
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021200
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.854.22749
X-RAY DIFFRACTIONr_mcbond_other2.8494.1992748
X-RAY DIFFRACTIONr_mcangle_it4.1336.2843431
X-RAY DIFFRACTIONr_mcangle_other4.1336.2863432
X-RAY DIFFRACTIONr_scbond_it3.9364.6772773
X-RAY DIFFRACTIONr_scbond_other3.934.6762772
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.0266.8174031
X-RAY DIFFRACTIONr_long_range_B_refined8.45880.10823105
X-RAY DIFFRACTIONr_long_range_B_other8.45180.1323054
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 163 -
Rwork0.346 3333 -
obs--96.98 %

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