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- PDB-6zl1: Crystal structure of human serum albumin in complex with the MCL-... -

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Basic information

Entry
Database: PDB / ID: 6zl1
TitleCrystal structure of human serum albumin in complex with the MCL-1 neutralizing Alphabody CMPX-383B
Components
  • Albumin
  • CMPX-383B
KeywordsDE NOVO PROTEIN / de novo protein design / 3 helical antiparallel coiled coil / cell penetrating Alphabody MCL-1 neutralizing Alphabody
Function / homology
Function and homology information


exogenous protein binding / Ciprofloxacin ADME / enterobactin binding / cellular response to calcium ion starvation / Heme biosynthesis / HDL remodeling / negative regulation of mitochondrial depolarization / Prednisone ADME / Heme degradation / Aspirin ADME ...exogenous protein binding / Ciprofloxacin ADME / enterobactin binding / cellular response to calcium ion starvation / 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 / cellular response to starvation / platelet alpha granule lumen / 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 / Golgi apparatus / endoplasmic reticulum / 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)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.272 Å
AuthorsPannecoucke, E. / Savvides, S.N. / Desmet, J. / Lasters, I.
Funding support Belgium, 1items
OrganizationGrant numberCountry
Research Foundation - Flanders (FWO) Belgium
CitationJournal: Sci Adv / Year: 2021
Title: Cell-penetrating Alphabody protein scaffolds for intracellular drug targeting.
Authors: Pannecoucke, E. / Van Trimpont, M. / Desmet, J. / Pieters, T. / Reunes, L. / Demoen, L. / Vuylsteke, M. / Loverix, S. / Vandenbroucke, K. / Alard, P. / Henderikx, P. / Deroo, S. / Baatz, F. ...Authors: Pannecoucke, E. / Van Trimpont, M. / Desmet, J. / Pieters, T. / Reunes, L. / Demoen, L. / Vuylsteke, M. / Loverix, S. / Vandenbroucke, K. / Alard, P. / Henderikx, P. / Deroo, S. / Baatz, F. / Lorent, E. / Thiolloy, S. / Somers, K. / McGrath, Y. / Van Vlierberghe, P. / Lasters, I. / Savvides, S.N.
History
DepositionJun 30, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 28, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Albumin
B: Albumin
C: CMPX-383B
D: CMPX-383B


Theoretical massNumber of molelcules
Total (without water)168,6434
Polymers168,6434
Non-polymers00
Water00
1
A: Albumin
C: CMPX-383B


Theoretical massNumber of molelcules
Total (without water)84,3222
Polymers84,3222
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1610 Å2
ΔGint-12 kcal/mol
Surface area33290 Å2
MethodPISA
2
B: Albumin
D: CMPX-383B


Theoretical massNumber of molelcules
Total (without water)84,3222
Polymers84,3222
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1670 Å2
ΔGint-13 kcal/mol
Surface area32900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.688, 231.346, 240.191
Angle α, β, γ (deg.)90, 90, 90
Int Tables number20
Space group name H-MC2221
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein Albumin


Mass: 69383.719 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: ALB, GIG20, GIG42, PRO0903, PRO1708, PRO2044, PRO2619, PRO2675, UNQ696/PRO1341
Production host: Homo sapiens (human) / References: UniProt: P02768
#2: Protein CMPX-383B


Mass: 14938.014 Da / Num. of mol.: 2 / Mutation: I92T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli BL21(DE3) (bacteria)
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: 2.59 Å3/Da / Density % sol: 52.48 % / Description: Plate-like
Crystal growTemperature: 310.15 K / Method: vapor diffusion, sitting drop / pH: 6.8
Details: 18% (w/v) PEG 3350, 0.1 M BIS-Tris pH 6.8, 0.2 M ammonium phosphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 24, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 3.272→115.673 Å / Num. obs: 24556 / % possible obs: 92.1 % / Redundancy: 4.8 % / Biso Wilson estimate: 88.79 Å2 / CC1/2: 0.993 / Net I/σ(I): 8.6
Reflection shellResolution: 3.272→3.389 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 0.52 / Num. unique obs: 1168 / CC1/2: 0.182 / CC star: 0.555 / % possible all: 44.11

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata scaling
PHASERphasing
Coot0.9 beta 2model building
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3MK8

3mk8


Resolution: 3.272→115.67 Å / Cor.coef. Fo:Fc: 0.898 / Cor.coef. Fo:Fc free: 0.871 / Cross valid method: THROUGHOUT / SU Rfree Blow DPI: 0.556
RfactorNum. reflection% reflectionSelection details
Rfree0.2809 1271 -RANDOM
Rwork0.2393 ---
obs0.2415 24556 91.8 %-
Displacement parametersBiso mean: 96.5 Å2
Baniso -1Baniso -2Baniso -3
1-4.1284 Å20 Å20 Å2
2---1.9367 Å20 Å2
3----2.1918 Å2
Refine analyzeLuzzati coordinate error obs: 0.55 Å
Refinement stepCycle: LAST / Resolution: 3.272→115.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8855 0 0 0 8855
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0099006HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0212361HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2630SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes1599HARMONIC5
X-RAY DIFFRACTIONt_it9006HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion1398SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies1HARMONIC1
X-RAY DIFFRACTIONt_ideal_dist_contact7733SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.35
X-RAY DIFFRACTIONt_other_torsion22.32
LS refinement shellResolution: 3.272→3.34 Å
RfactorNum. reflection% reflection
Rfree0.2883 20 -
Rwork0.2119 --
obs--32.04 %
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)
12.16590.83912.20460.67950.67631.88390.38790.24550.25920.2455-0.4162-0.80490.2592-0.80490.02830.0987-0.25780.19390.1211-0.1555-0.1454-6.2188-16.092323.8182
21.46380.2134-1.0690.9428-1.44021.62650.31410.0827-0.40810.0827-0.42580.8574-0.40810.85740.11160.1269-0.2796-0.11580.20090.0916-0.17967.181448.03329.2984
31.50481.56515.2886.12874.79948.08590.09660.06840.20760.06840.28710.2030.20760.203-0.38370.0198-0.17090.0449-0.142-0.05820.153724.25515.907840.9178
42.76140.7304-4.01430.9047-1.65327.75560.0148-0.14020.0869-0.14020.2349-0.09160.0869-0.0916-0.2497-0.1255-0.0862-0.0954-0.15480.01140.2436-22.216629.491849.1603
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|29 - A|608 }A29 - 608
2X-RAY DIFFRACTION2{ B|29 - B|607 }B29 - 607
3X-RAY DIFFRACTION3{ C|3 - C|144 }C3 - 144
4X-RAY DIFFRACTION4{ D|2 - D|144 }D2 - 144

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