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- PDB-3zy7: Crystal structure of computationally redesigned gamma-adaptin app... -

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Basic information

Entry
Database: PDB / ID: 3zy7
TitleCrystal structure of computationally redesigned gamma-adaptin appendage domain forming a symmetric homodimer
ComponentsAP-1 COMPLEX SUBUNIT GAMMA-1AP-1 transcription factor
KeywordsENDOCYTOSIS / PROTEIN DESIGN / COMPUTATIONAL DESIGN
Function / homology
Function and homology information


basolateral protein secretion / AP-1 adaptor complex / endosome to melanosome transport / positive regulation of natural killer cell degranulation / Lysosome Vesicle Biogenesis / platelet dense granule organization / melanosome assembly / Golgi to lysosome transport / Golgi to vacuole transport / Golgi Associated Vesicle Biogenesis ...basolateral protein secretion / AP-1 adaptor complex / endosome to melanosome transport / positive regulation of natural killer cell degranulation / Lysosome Vesicle Biogenesis / platelet dense granule organization / melanosome assembly / Golgi to lysosome transport / Golgi to vacuole transport / Golgi Associated Vesicle Biogenesis / GTP-dependent protein binding / clathrin adaptor activity / MHC class II antigen presentation / clathrin-coated vesicle / positive regulation of natural killer cell mediated cytotoxicity / kinesin binding / clathrin-coated pit / vesicle-mediated transport / trans-Golgi network membrane / intracellular protein transport / trans-Golgi network / recycling endosome / small GTPase binding / early endosome / lysosomal membrane / intracellular membrane-bounded organelle / perinuclear region of cytoplasm / Golgi apparatus / cytosol
Similarity search - Function
Gamma-adaptin ear (GAE) domain / Adaptor protein complex AP-1, gamma subunit / Gamma-adaptin ear (GAE) domain / Gamma-adaptin ear (GAE) domain profile. / Clathrin adaptor, alpha/beta/gamma-adaptin, appendage, Ig-like subdomain / Adaptin C-terminal domain / Adaptin C-terminal domain / Clathrin/coatomer adaptor, adaptin-like, N-terminal / Adaptin N terminal region / Clathrin adaptor, appendage, Ig-like subdomain superfamily ...Gamma-adaptin ear (GAE) domain / Adaptor protein complex AP-1, gamma subunit / Gamma-adaptin ear (GAE) domain / Gamma-adaptin ear (GAE) domain profile. / Clathrin adaptor, alpha/beta/gamma-adaptin, appendage, Ig-like subdomain / Adaptin C-terminal domain / Adaptin C-terminal domain / Clathrin/coatomer adaptor, adaptin-like, N-terminal / Adaptin N terminal region / Clathrin adaptor, appendage, Ig-like subdomain superfamily / Armadillo-like helical / Armadillo-type fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
ISOPROPYL ALCOHOL / DI(HYDROXYETHYL)ETHER / AP-1 complex subunit gamma-1
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.09 Å
AuthorsStranges, P.B. / Machius, M. / Miley, M.J. / Tripathy, A. / Kuhlman, B.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Computational Design of a Symmetric Homodimer Using Beta-Strand Assembly.
Authors: Stranges, P.B. / Machius, M. / Miley, M.J. / Tripathy, A. / Kuhlman, B.
History
DepositionAug 17, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 28, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2012Group: Other
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AP-1 COMPLEX SUBUNIT GAMMA-1
B: AP-1 COMPLEX SUBUNIT GAMMA-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6076
Polymers27,2752
Non-polymers3324
Water5,368298
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1720 Å2
ΔGint-3.3 kcal/mol
Surface area12090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.636, 44.248, 53.017
Angle α, β, γ (deg.)90.00, 91.91, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein AP-1 COMPLEX SUBUNIT GAMMA-1 / AP-1 transcription factor / REDESIGNED CLATHRIN ADAPTOR AP1 / ADAPTER-RELATED PROTEIN CO ADAPTOR PROTEIN COMPLEX AP-1 SUBUNIT ...REDESIGNED CLATHRIN ADAPTOR AP1 / ADAPTER-RELATED PROTEIN CO ADAPTOR PROTEIN COMPLEX AP-1 SUBUNIT GAMMA-1 / CLATHRIN ASSEMBLY PROTEIN COMPLEX 1 GAMMA-1 LARGE CHAIN / GAMMA-ADAPTIN / GAMMA1-ADAPTIN / GOLGI ADAPTOR HA1/AP1 ADAPTIN SUBUNIT GAMMA-1


Mass: 13637.434 Da / Num. of mol.: 2
Fragment: COMPUTATIONALLY REDESIGNED GAMMA-ADAPTIN APPENDAGE DOMAIN, RESIDUES 704-822
Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PQE-80L MBP FUSION VECTOR / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P22892
#2: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL / Isopropyl alcohol


Mass: 60.095 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 298 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, SER 711 TO ASP ENGINEERED RESIDUE IN CHAIN A, LYS 712 TO ALA ...ENGINEERED RESIDUE IN CHAIN A, SER 711 TO ASP ENGINEERED RESIDUE IN CHAIN A, LYS 712 TO ALA ENGINEERED RESIDUE IN CHAIN A, ASN 713 TO LEU ENGINEERED RESIDUE IN CHAIN A, TYR 800 TO PHE ENGINEERED RESIDUE IN CHAIN A, HIS 802 TO TRP ENGINEERED RESIDUE IN CHAIN A, LYS 803 TO ASN ENGINEERED RESIDUE IN CHAIN A, SER 805 TO TYR ENGINEERED RESIDUE IN CHAIN A, ALA 806 TO LYS ENGINEERED RESIDUE IN CHAIN A, MET 807 TO VAL ENGINEERED RESIDUE IN CHAIN A, ASP 809 TO SER ENGINEERED RESIDUE IN CHAIN A, LEU 810 TO GLU ENGINEERED RESIDUE IN CHAIN B, SER 711 TO ASP ENGINEERED RESIDUE IN CHAIN B, LYS 712 TO ALA ENGINEERED RESIDUE IN CHAIN B, ASN 713 TO LEU ENGINEERED RESIDUE IN CHAIN B, TYR 800 TO PHE ENGINEERED RESIDUE IN CHAIN B, HIS 802 TO TRP ENGINEERED RESIDUE IN CHAIN B, LYS 803 TO ASN ENGINEERED RESIDUE IN CHAIN B, SER 805 TO TYR ENGINEERED RESIDUE IN CHAIN B, ALA 806 TO LYS ENGINEERED RESIDUE IN CHAIN B, MET 807 TO VAL ENGINEERED RESIDUE IN CHAIN B, ASP 809 TO SER ENGINEERED RESIDUE IN CHAIN B, LEU 810 TO GLU

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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: 2.2 Å3/Da / Density % sol: 43.5 % / Description: NONE
Crystal growpH: 5
Details: PROTEIN SOLUTION: 20MM MES PH 6M 150MM NACL WELL SOLUTION: 0.1M NA ACETATE PH 5, 20% (W/V) PEG 8K, 6% (V/V) 2-PROPANOL CRYOPROTECTANT: WELL SOLUTION PLUS 15% (V/V) ETHYLENE GLYCOL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.9184
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 26, 2011 / Details: K-B PAIR OF BIOMORPH MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.09→23.14 Å / Num. obs: 90534 / % possible obs: 92.6 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 11.74 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 33.1
Reflection shellResolution: 1.09→1.1 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 1.9 / % possible all: 44.6

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2A7B

2a7b


Resolution: 1.09→23.135 Å / SU ML: 0.24 / σ(F): 0.27 / Phase error: 17.48 / Stereochemistry target values: ML
Details: RESIDUES -1 TO 0 AND 23-26 ARE DISORDERED IN CHAINS A AND B
RfactorNum. reflection% reflection
Rfree0.1806 4502 5 %
Rwork0.158 --
obs0.1592 90295 92.33 %
Solvent computationShrinkage radii: 0.77 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.288 Å2 / ksol: 0.406 e/Å3
Displacement parametersBiso mean: 15.8 Å2
Baniso -1Baniso -2Baniso -3
1-0.4479 Å20 Å2-0.0563 Å2
2---0.9722 Å20 Å2
3---0.5243 Å2
Refinement stepCycle: LAST / Resolution: 1.09→23.135 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1842 0 22 298 2162
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112175
X-RAY DIFFRACTIONf_angle_d1.3993001
X-RAY DIFFRACTIONf_dihedral_angle_d15.058821
X-RAY DIFFRACTIONf_chiral_restr0.082342
X-RAY DIFFRACTIONf_plane_restr0.006403
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.09-1.10240.2975890.28171343X-RAY DIFFRACTION44
1.1024-1.11540.2956730.26191664X-RAY DIFFRACTION54
1.1154-1.1290.2931970.24031914X-RAY DIFFRACTION61
1.129-1.14330.27471040.23042113X-RAY DIFFRACTION69
1.1433-1.15830.25431260.20932406X-RAY DIFFRACTION77
1.1583-1.17420.25771400.19562628X-RAY DIFFRACTION86
1.1742-1.1910.21540.18112861X-RAY DIFFRACTION93
1.191-1.20870.17781410.18433059X-RAY DIFFRACTION99
1.2087-1.22760.20971530.17163110X-RAY DIFFRACTION100
1.2276-1.24770.20431610.15753046X-RAY DIFFRACTION100
1.2477-1.26930.18091680.15063091X-RAY DIFFRACTION100
1.2693-1.29230.16631590.14643069X-RAY DIFFRACTION100
1.2923-1.31720.181700.14233043X-RAY DIFFRACTION100
1.3172-1.34410.16371470.13983083X-RAY DIFFRACTION100
1.3441-1.37330.15131550.13733074X-RAY DIFFRACTION99
1.3733-1.40520.17111590.13483067X-RAY DIFFRACTION99
1.4052-1.44040.18561530.12773095X-RAY DIFFRACTION100
1.4404-1.47930.15161590.12173068X-RAY DIFFRACTION99
1.4793-1.52280.16111690.12463081X-RAY DIFFRACTION100
1.5228-1.5720.14571570.12743104X-RAY DIFFRACTION100
1.572-1.62820.16221650.12783071X-RAY DIFFRACTION100
1.6282-1.69330.15991850.13243068X-RAY DIFFRACTION100
1.6933-1.77040.17891500.13623126X-RAY DIFFRACTION100
1.7704-1.86370.17111670.14263072X-RAY DIFFRACTION100
1.8637-1.98040.17651520.14273109X-RAY DIFFRACTION100
1.9804-2.13320.16381870.14213073X-RAY DIFFRACTION100
2.1332-2.34770.17171650.14213119X-RAY DIFFRACTION100
2.3477-2.68690.14691490.15823141X-RAY DIFFRACTION100
2.6869-3.38360.18141840.17123109X-RAY DIFFRACTION99
3.3836-23.14050.20841640.19162986X-RAY DIFFRACTION93

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