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- PDB-3zhf: gamma 2 adaptin EAR domain crystal structure with preS1 site1 pep... -

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Basic information

Entry
Database: PDB / ID: 3zhf
Titlegamma 2 adaptin EAR domain crystal structure with preS1 site1 peptide NPDWDFN
Components
  • AP-1 COMPLEX SUBUNIT GAMMA-LIKE 2
  • LARGE ENVELOPE PROTEIN
KeywordsPROTEIN TRANSPORT/VIRAL PROTEIN / PROTEIN TRANSPORT-VIRAL PROTEIN COMPLEX / GAE
Function / homology
Function and homology information


AP-1 adaptor complex / Golgi to vacuole transport / caveolin-mediated endocytosis of virus by host cell / clathrin adaptor activity / Golgi-associated vesicle / Lysosome Vesicle Biogenesis / transport vesicle / vesicle-mediated transport / intracellular protein transport / endosome membrane ...AP-1 adaptor complex / Golgi to vacuole transport / caveolin-mediated endocytosis of virus by host cell / clathrin adaptor activity / Golgi-associated vesicle / Lysosome Vesicle Biogenesis / transport vesicle / vesicle-mediated transport / intracellular protein transport / endosome membrane / Golgi membrane / fusion of virus membrane with host endosome membrane / synapse / virion attachment to host cell / virion membrane / Golgi apparatus / membrane
Similarity search - Function
Gamma-adaptin ear (GAE) domain / Large envelope protein S / Major surface antigen from hepadnavirus / 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 ...Gamma-adaptin ear (GAE) domain / Large envelope protein S / Major surface antigen from hepadnavirus / 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
DI(HYDROXYETHYL)ETHER / AP-1 complex subunit gamma-like 2 / Large envelope protein
Similarity search - Component
Biological speciesHomo sapiens (human)
HEPATITIS B VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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
DepositionDec 21, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 10, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2013Group: Database references / Source and taxonomy
Revision 1.2Jul 24, 2013Group: Database references
Revision 1.3Jul 31, 2013Group: Source and taxonomy
Revision 1.4Aug 28, 2013Group: Database references
Revision 1.5Jul 1, 2015Group: Data collection
Revision 1.6Mar 7, 2018Group: Data collection / Source and taxonomy / Category: diffrn_source / entity_src_gen
Item: _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_gene_src_scientific_name ..._diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.7Oct 23, 2019Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: pdbx_database_status / struct_conn / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.8Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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 1.9Nov 20, 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
A: AP-1 COMPLEX SUBUNIT GAMMA-LIKE 2
B: LARGE ENVELOPE PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,8624
Polymers14,6942
Non-polymers1682
Water1,51384
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1040 Å2
ΔGint-8.8 kcal/mol
Surface area8500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.841, 37.457, 105.484
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


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 BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: O75843
#2: Protein/peptide LARGE ENVELOPE PROTEIN / HBV L PROTEIN


Mass: 930.940 Da / Num. of mol.: 1 / Fragment: PRES1 DOMAIN, RESIDUES 85-91 / Source method: obtained synthetically / Details: AMIDATED C-TERMINUS, CARBOXYLATED N-TERMINUS / Source: (synth.) HEPATITIS B VIRUS / References: UniProt: Q67953
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsAMINO GROUP (NH2): PEPTIDE C TERMINUS IS AMIDATED
Sequence detailsGGS IS A CLONING ARTEFACT AT THE PROTEIN N-TERMINUS

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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: 2.51 Å3/Da / Density % sol: 51.07 % / Description: NONE
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), PEPTIDE WAS AT ABOUT 50 FOLD MOLAR EXCESS

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 1.2395
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 20, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2395 Å / Relative weight: 1
ReflectionResolution: 1.7→37.46 Å / Num. obs: 15669 / % possible obs: 98.8 % / Observed criterion σ(I): 2.7 / Redundancy: 4.1 % / Biso Wilson estimate: 20.34 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 17.3
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 2.7 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.8_1069)refinement
XDSdata reduction
SCALAdata scaling
DIMPLEphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4BCX

4bcx


Resolution: 1.7→35.298 Å / SU ML: 0.18 / σ(F): 1.34 / Phase error: 23.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2257 779 5 %
Rwork0.1896 --
obs0.1913 15598 98.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→35.298 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1026 0 11 84 1121
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061115
X-RAY DIFFRACTIONf_angle_d1.0811527
X-RAY DIFFRACTIONf_dihedral_angle_d14.208429
X-RAY DIFFRACTIONf_chiral_restr0.072170
X-RAY DIFFRACTIONf_plane_restr0.005204
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.80650.26971230.23982426X-RAY DIFFRACTION99
1.8065-1.9460.25021330.19182418X-RAY DIFFRACTION98
1.946-2.14180.21861350.17392422X-RAY DIFFRACTION99
2.1418-2.45170.26121330.1782445X-RAY DIFFRACTION98
2.4517-3.08860.2241330.19442495X-RAY DIFFRACTION99
3.0886-35.30520.20611220.18862613X-RAY DIFFRACTION98

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