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- PDB-2ymt: gamma 2 adaptin EAR domain crystal structure with phage peptide G... -

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Basic information

Entry
Database: PDB / ID: 2ymt
Titlegamma 2 adaptin EAR domain crystal structure with phage peptide GEEWGPWV
Components
  • AP-1 COMPLEX SUBUNIT GAMMA-LIKE 2
  • PHAGE DISPLAY DERIVED GAMMA 2 ADAPTIN EAR DOMAIN BINDING PEPTIDE
KeywordsPROTEIN TRANSPORT
Function / homology
Function and homology information


AP-1 adaptor complex / Golgi to vacuole transport / clathrin adaptor activity / Lysosome Vesicle Biogenesis / Golgi-associated vesicle / vesicle-mediated transport / transport vesicle / intracellular protein transport / endosome membrane / Golgi membrane ...AP-1 adaptor complex / Golgi to vacuole transport / clathrin adaptor activity / Lysosome Vesicle Biogenesis / Golgi-associated vesicle / vesicle-mediated transport / transport vesicle / intracellular protein transport / endosome membrane / Golgi membrane / Golgi apparatus / membrane
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 ...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
1,3-PROPANDIOL / AP-1 complex subunit gamma-like 2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.802 Å
AuthorsJuergens, M.C. / Voros, J. / Rautureau, G. / Shepherd, D. / Pye, V.E. / Muldoon, J. / Johnson, C.M. / Ashcroft, A. / Freund, S.M.V. / Ferguson, N.
CitationJournal: Nat.Chem.Biol. / Year: 2013
Title: The Hepatitis B Virus Pres1 Domain Hijacks Host Trafficking Proteins by Motif Mimicry.
Authors: Jurgens, M.C. / Voros, J. / Rautureau, G.J.P. / Shepherd, D.A. / Pye, V.E. / Muldoon, J. / Johnson, C.M. / Ashcroft, A.E. / Freund, S.M.V. / Ferguson, N.
History
DepositionOct 10, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 10, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2013Group: Database references
Revision 1.2Jul 24, 2013Group: Database references
Revision 1.3Aug 28, 2013Group: Database references
Revision 1.4Jul 12, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.5Dec 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_conn / 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_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Nov 20, 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: AP-1 COMPLEX SUBUNIT GAMMA-LIKE 2
B: PHAGE DISPLAY DERIVED GAMMA 2 ADAPTIN EAR DOMAIN BINDING PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,7963
Polymers14,7202
Non-polymers761
Water2,252125
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1310 Å2
ΔGint-5.5 kcal/mol
Surface area7120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.803, 37.772, 105.471
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein AP-1 COMPLEX SUBUNIT GAMMA-LIKE 2 / GAMMA2-ADAPTIN / G2AD / GAMMA 2 ADAPTIN EAR DOMAIN


Mass: 13762.746 Da / Num. of mol.: 1 / Fragment: EAR DOMAIN, RESIDUES 665-785
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): C41 / References: UniProt: O75843
#2: Protein/peptide PHAGE DISPLAY DERIVED GAMMA 2 ADAPTIN EAR DOMAIN BINDING PEPTIDE


Mass: 957.019 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#3: Chemical ChemComp-PDO / 1,3-PROPANDIOL


Mass: 76.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / 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: 2.53 Å3/Da / Density % sol: 51.42 %
Crystal growpH: 6.5
Details: 100 MM MES/IMIDAZOLE PH 6.5, 0.02 M 1,6-HEXANEDIOL, 0.02 M 1-BUTANOL, 0.02 M (RS)-1,2- PROPANEDIOL, 0.02 M 2-PROPANOL, 0.02 M 1,4-BUTANEDIOL, 0.02 M 1,3-PROPANEDIOL, 10% (W/V) PEG 20000 AND ...Details: 100 MM MES/IMIDAZOLE PH 6.5, 0.02 M 1,6-HEXANEDIOL, 0.02 M 1-BUTANOL, 0.02 M (RS)-1,2- PROPANEDIOL, 0.02 M 2-PROPANOL, 0.02 M 1,4-BUTANEDIOL, 0.02 M 1,3-PROPANEDIOL, 10% (W/V) PEG 20000 AND 24% (V/V) PEG400 (USING A 2:1 RATIO OF PROTEIN TO MOTHER LIQUOR)

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418
DetectorType: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Sep 25, 2012 / Details: OSMIC BLUE CONFOCAL MIRRORS
RadiationMonochromator: OSMIC VARIMAX HR OPTICS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→30.71 Å / Num. obs: 13212 / % possible obs: 97.7 % / Observed criterion σ(I): 2.7 / Redundancy: 6.4 % / Biso Wilson estimate: 17.2 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 11.6
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2.7 / % possible all: 8

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4BCX

4bcx


Resolution: 1.802→30.708 Å / SU ML: 0.19 / σ(F): 1.34 / Phase error: 22.19 / Stereochemistry target values: ML
Details: SAME KSOL AND BSOL ISSUE AS FOR THE 4BCX ENTRY. THEY DO NOT APPEAR IN THE SOFTWARE OUTPUT. PDB COMMENT WAS THAT THIS IS KNOWN AND NULL IS OK TO PUT INSTEAD OF N A AS THIS IS NOT ACCEPTED DURING DEPOSITION.
RfactorNum. reflection% reflection
Rfree0.242 640 4.9 %
Rwork0.185 --
obs0.1876 13166 97.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 0 Å2 / ksol: 0 e/Å3
Displacement parametersBiso mean: 18.1 Å2
Refinement stepCycle: LAST / Resolution: 1.802→30.708 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1021 0 5 125 1151
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061078
X-RAY DIFFRACTIONf_angle_d1.0981479
X-RAY DIFFRACTIONf_dihedral_angle_d12.295408
X-RAY DIFFRACTIONf_chiral_restr0.069168
X-RAY DIFFRACTIONf_plane_restr0.006195
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8016-1.94070.29011210.212215X-RAY DIFFRACTION89
1.9407-2.1360.23791230.17932514X-RAY DIFFRACTION100
2.136-2.4450.22451260.18262538X-RAY DIFFRACTION100
2.445-3.07990.24491220.19832570X-RAY DIFFRACTION100
3.0799-30.71220.23921480.17632689X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -2.5745 Å / Origin y: -3.2126 Å / Origin z: 14.8178 Å
111213212223313233
T0.0829 Å20.0039 Å2-0.0017 Å2-0.1103 Å2-0.0092 Å2--0.0787 Å2
L0.6237 °2-0.168 °2-0.269 °2-1.4811 °20.8746 °2--1.8991 °2
S-0.0177 Å °0.0783 Å °0.0144 Å °-0.0387 Å °-0.0851 Å °0.1094 Å °-0.0329 Å °-0.2522 Å °0.0625 Å °
Refinement TLS groupSelection details: ALL

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