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- PDB-9cdt: Crystal Structure of MCL-1-Peptide Complex -

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Basic information

Entry
Database: PDB / ID: 9cdt
TitleCrystal Structure of MCL-1-Peptide Complex
Components
  • Induced myeloid leukemia cell differentiation protein Mcl-1
  • MCB_D2 peptide
KeywordsAPOPTOSIS / De novo design / deep learning / macro cycle / MCL-1 / apotosis regulator
Function / homology
Function and homology information


positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / cell fate determination / cellular homeostasis / mitochondrial fusion / Bcl-2 family protein complex / BH3 domain binding / negative regulation of anoikis / protein transmembrane transporter activity / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / extrinsic apoptotic signaling pathway in absence of ligand ...positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / cell fate determination / cellular homeostasis / mitochondrial fusion / Bcl-2 family protein complex / BH3 domain binding / negative regulation of anoikis / protein transmembrane transporter activity / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / extrinsic apoptotic signaling pathway in absence of ligand / response to cytokine / negative regulation of autophagy / release of cytochrome c from mitochondria / intrinsic apoptotic signaling pathway in response to DNA damage / Signaling by ALK fusions and activated point mutants / positive regulation of neuron apoptotic process / channel activity / Interleukin-4 and Interleukin-13 signaling / regulation of apoptotic process / mitochondrial outer membrane / positive regulation of apoptotic process / protein heterodimerization activity / DNA damage response / negative regulation of apoptotic process / mitochondrion / nucleoplasm / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
Apoptosis regulator, Mcl-1 / Apoptosis regulator, Bcl-2, BH3 motif, conserved site / Apoptosis regulator, Bcl-2 family BH3 motif signature. / Apoptosis regulator, Bcl-2, BH1 motif, conserved site / Apoptosis regulator, Bcl-2 family BH1 motif signature. / Apoptosis regulator, Bcl-2, BH2 motif, conserved site / Apoptosis regulator, Bcl-2 family BH2 motif signature. / Bcl-2 family / BCL (B-Cell lymphoma); contains BH1, BH2 regions / Bcl2-like ...Apoptosis regulator, Mcl-1 / Apoptosis regulator, Bcl-2, BH3 motif, conserved site / Apoptosis regulator, Bcl-2 family BH3 motif signature. / Apoptosis regulator, Bcl-2, BH1 motif, conserved site / Apoptosis regulator, Bcl-2 family BH1 motif signature. / Apoptosis regulator, Bcl-2, BH2 motif, conserved site / Apoptosis regulator, Bcl-2 family BH2 motif signature. / Bcl-2 family / BCL (B-Cell lymphoma); contains BH1, BH2 regions / Bcl2-like / Bcl-2, Bcl-2 homology region 1-3 / Apoptosis regulator proteins, Bcl-2 family / BCL2-like apoptosis inhibitors family profile. / Bcl-2-like superfamily
Similarity search - Domain/homology
Induced myeloid leukemia cell differentiation protein Mcl-1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsBera, A.K. / Rettie, S. / Kang, A. / Bhardwaj, G.
Funding support United States, 2items
OrganizationGrant numberCountry
Defense Advanced Research Projects Agency (DARPA) United States
Defense Threat Reduction Agency (DTRA) United States
CitationJournal: Nat.Chem.Biol. / Year: 2025
Title: Accurate de novo design of high-affinity protein-binding macrocycles using deep learning.
Authors: Rettie, S.A. / Juergens, D. / Adebomi, V. / Bueso, Y.F. / Zhao, Q. / Leveille, A.N. / Liu, A. / Bera, A.K. / Wilms, J.A. / Uffing, A. / Kang, A. / Brackenbrough, E. / Lamb, M. / Gerben, S.R. ...Authors: Rettie, S.A. / Juergens, D. / Adebomi, V. / Bueso, Y.F. / Zhao, Q. / Leveille, A.N. / Liu, A. / Bera, A.K. / Wilms, J.A. / Uffing, A. / Kang, A. / Brackenbrough, E. / Lamb, M. / Gerben, S.R. / Murray, A. / Levine, P.M. / Schneider, M. / Vasireddy, V. / Ovchinnikov, S. / Weiergraber, O.H. / Willbold, D. / Kritzer, J.A. / Mougous, J.D. / Baker, D. / DiMaio, F. / Bhardwaj, G.
History
DepositionJun 25, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 2, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Induced myeloid leukemia cell differentiation protein Mcl-1
B: MCB_D2 peptide


Theoretical massNumber of molelcules
Total (without water)19,0762
Polymers19,0762
Non-polymers00
Water55831
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1180 Å2
ΔGint-14 kcal/mol
Surface area8340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.484, 75.366, 43.371
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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Components

#1: Protein Induced myeloid leukemia cell differentiation protein Mcl-1 / Bcl-2-like protein 3 / Bcl2-L-3 / Bcl-2-related protein EAT/mcl1 / mcl1/EAT


Mass: 17408.844 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MCL1, BCL2L3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q07820
#2: Protein/peptide MCB_D2 peptide


Mass: 1666.891 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / 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: 2.25 Å3/Da / Density % sol: 45.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M Sodium chloride, 0.1 M Bis-Tris pH 6.5, and 25% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.9201 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 12, 2024 / Details: KB bimorph mirrors
RadiationMonochromator: Si(111) DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9201 Å / Relative weight: 1
ReflectionResolution: 2.1→33.43 Å / Num. obs: 10245 / % possible obs: 97.25 % / Redundancy: 7.8 % / Biso Wilson estimate: 41.81 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.035 / Net I/σ(I): 11.85
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.86 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 1470 / CC1/2: 0.85 / Rpim(I) all: 0.324 / % possible all: 99.93

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Processing

Software
NameVersionClassification
PHENIXdev_4761refinement
PHENIXdev_4761refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→33.43 Å / SU ML: 0.3083 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 29.6455
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2716 1025 10 %
Rwork0.2164 9220 -
obs0.2218 10245 97.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 55 Å2
Refinement stepCycle: LAST / Resolution: 2.1→33.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1319 0 0 31 1350
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00291342
X-RAY DIFFRACTIONf_angle_d0.47671807
X-RAY DIFFRACTIONf_chiral_restr0.0348202
X-RAY DIFFRACTIONf_plane_restr0.0033230
X-RAY DIFFRACTIONf_dihedral_angle_d3.8093179
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.210.42211470.32351325X-RAY DIFFRACTION99.93
2.21-2.350.34381200.28431074X-RAY DIFFRACTION81.28
2.35-2.530.29531490.25691339X-RAY DIFFRACTION100
2.53-2.780.29081470.24591327X-RAY DIFFRACTION100
2.78-3.190.28491500.24531347X-RAY DIFFRACTION99.93
3.19-4.010.29461520.19821373X-RAY DIFFRACTION99.8
4.02-33.430.21791600.18451435X-RAY DIFFRACTION99.44
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)
15.02760738724-0.1885554350150.9028906972413.5547421112-0.1194552329913.103672682970.131618574894-0.663017743540.1778757098550.581165562802-0.1684659894380.2813885758060.164160844589-0.1889198732450.04339015851060.372204469542-0.04958845793510.08449145369280.370650947754-0.03225401605520.339179685929-9.2067066106212.9201087887-11.8864354757
20.5047213803910.00858616857107-0.4739813472240.114721858552-0.02919363112890.44960156427-0.2704544284332.0383082711-0.0272429886732-1.98818738984-0.4543427314310.2983755205430.14260320768-0.651603957207-0.03104786631890.717587195526-0.0119559983607-0.09710777647920.7992308410570.03099678379190.6239749405-9.364593295349.12960746857-29.2341903932
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain A and resseq 0:149)AA0 - 1491 - 150
22(chain B and resseq 152:167)BB152 - 1671 - 16

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