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- PDB-7oub: High resolution structure of Alpha-1-acid glycoprotein bound to p... -

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Basic information

Entry
Database: PDB / ID: 7oub
TitleHigh resolution structure of Alpha-1-acid glycoprotein bound to potent anti-tumour compound UCN-01
ComponentsAlpha-1-acid glycoprotein 2
KeywordsPROTEIN TRANSPORT / AGP2 / ORM2 / lipocalin / complex / Alpha-1-acid Glycoprotein / UCN-01
Function / homology
Function and homology information


positive regulation of interleukin-1 production / regulation of immune system process / platelet alpha granule lumen / positive regulation of interleukin-1 beta production / acute-phase response / specific granule lumen / positive regulation of tumor necrosis factor production / azurophil granule lumen / Platelet degranulation / : ...positive regulation of interleukin-1 production / regulation of immune system process / platelet alpha granule lumen / positive regulation of interleukin-1 beta production / acute-phase response / specific granule lumen / positive regulation of tumor necrosis factor production / azurophil granule lumen / Platelet degranulation / : / blood microparticle / Neutrophil degranulation / extracellular space / extracellular exosome / extracellular region
Similarity search - Function
Alpha-1-acid glycoprotein / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin
Similarity search - Domain/homology
7-HYDROXYSTAUROSPORINE / Alpha-1-acid glycoprotein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 Å
AuthorsLandin, E.J.B. / Williams, C. / Crump, M.P.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/L01386X/1 United Kingdom
Commonwealth Scholarship Commission (United Kingdom)BDCS-2017-50 United Kingdom
CitationJournal: J.Biol.Chem. / Year: 2021
Title: The structural basis for high affinity binding of alpha 1-acid glycoprotein to the potent antitumor compound UCN-01.
Authors: Landin, E.J.B. / Williams, C. / Ryan, S.A. / Bochel, A. / Akter, N. / Redfield, C. / Sessions, R.B. / Dedi, N. / Taylor, R.J. / Crump, M.P.
History
DepositionJun 11, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 1, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 22, 2021Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Alpha-1-acid glycoprotein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0272
Polymers22,5441
Non-polymers4831
Water4,017223
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area870 Å2
ΔGint3 kcal/mol
Surface area9290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.270, 88.270, 53.840
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Alpha-1-acid glycoprotein 2 / AGP 2 / Orosomucoid-2 / OMD 2


Mass: 22544.227 Da / Num. of mol.: 1 / Mutation: C149R
Source method: isolated from a genetically manipulated source
Details: MAHHHHHHSSGLEVLFQGP are vector derived. During purification the protein is cleaved leaving GP from the vector (-1-0) and the mature native protein starts at the Q (1) of QIP after the ...Details: MAHHHHHHSSGLEVLFQGP are vector derived. During purification the protein is cleaved leaving GP from the vector (-1-0) and the mature native protein starts at the Q (1) of QIP after the cleavage tag. The C-terminal His197 is not visible in the crystal structure.
Source: (gene. exp.) Homo sapiens (human) / Gene: ORM2, AGP2 / Plasmid: pOPINF / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P19652
#2: Chemical ChemComp-UCN / 7-HYDROXYSTAUROSPORINE


Mass: 482.530 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H26N4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 223 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.95 Å3/Da / Density % sol: 58.25 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.4 / Details: 0.1M HEPES 1.4M sodium acetate / PH range: 0.1

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 26, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 1.82→76.44 Å / Num. obs: 21541 / % possible obs: 99.68 % / Redundancy: 18.4 % / Biso Wilson estimate: 21.17 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.014 / Rrim(I) all: 0.06 / Net I/σ(I): 34.3
Reflection shellResolution: 1.82→4.94 Å / Redundancy: 10.3 % / Rmerge(I) obs: 0.16 / Mean I/σ(I) obs: 9.9 / Num. unique obs: 1034 / CC1/2: 0.986 / Rpim(I) all: 0.051 / Rrim(I) all: 0.169 / % possible all: 96

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Processing

Software
NameVersionClassification
PHENIX1.18_3855refinement
PDB_EXTRACT3.27data extraction
XDS2 0.5.902data reduction
DIALS1.14data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3apu

3apu


Resolution: 1.82→44.13 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.44 / Phase error: 19.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1768 986 4.58 %
Rwork0.156 20528 -
obs0.157 21514 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 88.08 Å2 / Biso mean: 30.2026 Å2 / Biso min: 10.62 Å2
Refinement stepCycle: final / Resolution: 1.82→44.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1439 0 36 223 1698
Biso mean--19.13 39.33 -
Num. residues----173
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.82-1.920.22451750.18942852302798
1.92-2.040.21791350.166128903025100
2.04-2.190.21611430.168929353078100
2.19-2.410.19991330.162829233056100
2.41-2.760.17821270.176929513078100
2.76-3.480.17931310.161629683099100
3.48-44.130.14111420.131930093151100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.75051.3399-0.15011.02070.66171.5068-0.30120.5925-0.2288-0.13930.29680.02030.3801-0.10430.06550.2165-0.0672-0.00880.203-0.00710.1547-16.386529.9675-4.6688
25.59881.3107-1.45264.1886-0.47022.5554-0.1651-0.1778-0.02170.11960.1112-0.1833-0.07660.2304-0.00420.04550.0144-0.01120.23350.00260.1682-3.853934.5793-0.8854
35.30531.336-1.15724.4125-0.08833.4292-0.41520.4221-0.5442-0.03970.1635-0.27140.33070.3530.11190.15580.01860.07370.3254-0.0680.2144-0.153228.8188-7.1644
47.02964.32490.98416.62983.02769.09-0.3201-0.311-2.25340.39540.2657-0.90950.91250.5978-0.30760.29950.02770.11580.1662-0.02190.4035-7.575521.4812-1.9825
54.1397-2.15870.47156.6073-2.84974.5941-0.18180.2325-0.0910.073-0.0365-0.16690.19570.04210.19770.1149-0.04410.01820.1557-0.02480.111-14.708930.4026-4.4202
64.67650.3226-1.23532.7615-2.34446.8951-0.1660.20590.2844-0.00090.0319-0.0192-0.0804-0.04530.12130.086-0.0309-0.03440.1102-0.02770.1104-17.255637.2237-0.1929
75.93092.6949-6.2312.6792-3.35287.8670.3591-0.37420.72320.3475-0.1119-0.0853-0.66920.364-0.21070.15-0.0349-0.02870.1759-0.02420.3272-11.399344.27142.3994
86.2185-6.8025-3.50062.03472.98384.31190.95251.6850.6788-1.5447-0.7222-0.4176-0.465-0.14220.01240.1984-0.1131-0.00760.62630.20320.52875.836342.2123-12.4675
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 1 through 36 )B1 - 36
2X-RAY DIFFRACTION2chain 'B' and (resid 37 through 56 )B37 - 56
3X-RAY DIFFRACTION3chain 'B' and (resid 57 through 84 )B57 - 84
4X-RAY DIFFRACTION4chain 'B' and (resid 85 through 96 )B85 - 96
5X-RAY DIFFRACTION5chain 'B' and (resid 97 through 116 )B97 - 116
6X-RAY DIFFRACTION6chain 'B' and (resid 117 through 150 )B117 - 150
7X-RAY DIFFRACTION7chain 'B' and (resid 151 through 164 )B151 - 164
8X-RAY DIFFRACTION8chain 'B' and (resid 165 through 173 )B165 - 173

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