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- PDB-2mj7: Solution NMR structure of beta-adaptin appendage domain of human ... -

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Basic information

Entry
Database: PDB / ID: 2mj7
TitleSolution NMR structure of beta-adaptin appendage domain of human adaptor protein complex 4 subunit beta, Northeast Structural Genomics Consortium (NESG) Target HR8998C
ComponentsAP-4 complex subunit beta-1
KeywordsTRANSPORT PROTEIN / Structural Genomics / NORTHEAST STRUCTURAL GENOMICS CONSORTIUM / NESG / PSI-Biology / Protein Structure Initiative
Function / homology
Function and homology information


AP-4 adaptor complex / clathrin adaptor complex / Lysosome Vesicle Biogenesis / clathrin binding / extrinsic component of membrane / Golgi Associated Vesicle Biogenesis / protein targeting / vesicle-mediated transport / trans-Golgi network membrane / endosome lumen ...AP-4 adaptor complex / clathrin adaptor complex / Lysosome Vesicle Biogenesis / clathrin binding / extrinsic component of membrane / Golgi Associated Vesicle Biogenesis / protein targeting / vesicle-mediated transport / trans-Golgi network membrane / endosome lumen / protein localization / trans-Golgi network / cytosol
Similarity search - Function
TATA-Binding Protein / Beta-adaptin appendage, C-terminal subdomain / AP-1/2/4 complex subunit beta / Beta2-adaptin appendage, C-terminal sub-domain / Beta2-adaptin appendage, C-terminal sub-domain / AP complex subunit beta / Clathrin/coatomer adaptor, adaptin-like, N-terminal / Adaptin N terminal region / TATA-Binding Protein / TBP domain superfamily ...TATA-Binding Protein / Beta-adaptin appendage, C-terminal subdomain / AP-1/2/4 complex subunit beta / Beta2-adaptin appendage, C-terminal sub-domain / Beta2-adaptin appendage, C-terminal sub-domain / AP complex subunit beta / Clathrin/coatomer adaptor, adaptin-like, N-terminal / Adaptin N terminal region / TATA-Binding Protein / TBP domain superfamily / Armadillo-like helical / Armadillo-type fold / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
AP-4 complex subunit beta-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsEletsky, A. / Rotshteyn, D.J. / Pederson, K. / Shastry, R. / Maglaqui, M. / Janjua, H. / Xiao, R. / Everett, J.K. / Montelione, G.T. / Prestegard, J.H. ...Eletsky, A. / Rotshteyn, D.J. / Pederson, K. / Shastry, R. / Maglaqui, M. / Janjua, H. / Xiao, R. / Everett, J.K. / Montelione, G.T. / Prestegard, J.H. / Szyperski, T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Solution NMR structure of beta-adaptin appendage domain of human adaptor protein complex 4 subunit beta, Northeast Structural Genomics Consortium (NESG) Target HR8998C
Authors: Eletsky, A. / Rotshteyn, D.J. / Pederson, K. / Shastry, R. / Maglaqui, M. / Janjua, H. / Xiao, R. / Everett, J.K. / Montelione, G.T. / Prestegard, J.H. / Szyperski, T.
History
DepositionDec 26, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 29, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: AP-4 complex subunit beta-1


Theoretical massNumber of molelcules
Total (without water)16,0041
Polymers16,0041
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein AP-4 complex subunit beta-1 / AP-4 adapter complex subunit beta / Adapter-related protein complex 4 subunit beta-1 / Beta subunit ...AP-4 adapter complex subunit beta / Adapter-related protein complex 4 subunit beta-1 / Beta subunit of AP-4 / Beta4-adaptin


Mass: 16004.169 Da / Num. of mol.: 1 / Fragment: UNP residues 610-739
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AP4B1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pMgK / References: UniProt: Q9Y6B7

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1142D 1H-15N HSQC
1242D 1H-13C HSQC aliphatic
1343D HNCO
1443D CBCA(CO)NH
1543D HN(CA)CB
1643D HN(CA)CO
1743D simutaneous 13C-aromatic,13C-aliphatic,15N edited 1H-1H NOESY
1842D 1H-13C HSQC aromatic
1943D HBHA(CO)NH
11043D HA(CO)NH
11143D HNCA
11243D (H)CCH-TOCSY aliphatic
11343D (H)CCH-COSY aliphatic
11443D (H)CCH-COSY aromatic
11532D 1H-15N long-range HSQC
21632D 1H-15N HSQC
31732D 1H-15N HSQC
41832D 1H-15N HSQC
51932D 1H-15N HSQC
62032D 1H-15N HSQC
12132D 1H-15N HSQC
22222D 1H-15N J-MODULATED HSQC
22322D 1H-15N J-MODULATED HSQC
22422D 1H-15N J-MODULATED HSQC
12512D 1H-13C CT-HSQC methyl

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Sample preparation

Details
Solution-IDContentsSolvent system
10.4 mM HR8998C NC5, 90% H2O/10% D2O90% H2O/10% D2O
20.2 mM HR8998C NC5, 4% PEG/hexanol, 80% H2O/20% D2O80% H2O/20% D2O
30.2 mM HR8998C NC5, Pf1 phage, 80% H2O/20% D2O80% H2O/20% D2O
40.2 mM HR8998C NC, 90% H2O/10% D2O90% H2O/10% D2O
Sample conditionspH: 6.5 / Pressure: ambient / Temperature: 295 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA7501
Agilent DD2AgilentDD26002
Varian INOVAVarianINOVA6003

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.3Brunger, Adams, Clore, Gros, Nilges and Readrefinement
CNS1.3Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNS1.3Brunger, Adams, Clore, Gros, Nilges and Readgeometry optimization
CYANA3Guntert, Mumenthaler and Wuthrichrefinement
CYANA3Guntert, Mumenthaler and Wuthrichgeometry optimization
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
AS-DP1Huang, Tejero, Powers and Montelionedata analysis
AS-DP1Huang, Tejero, Powers and Montelionerefinement
AS-DP1Huang, Tejero, Powers and Montelionestructure solution
AutoAssign2.3.0Zimmerman, Moseley, Kulikowski and Montelionedata analysis
AutoAssign2.3.0Zimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
XEASYBartels et al.data analysis
PROSA6.4Guntertprocessing
VnmrJVariancollection
SparkyGoddarddata analysis
TALOSNShen, Cornilescu, Delaglio and Baxgeometry optimization
CARA1.8.4Keller and Wuthrichchemical shift assignment
CARA1.8.4Keller and Wuthrichdata analysis
CARA1.8.4Keller and Wuthrichpeak picking
PSVS1.5Bhattacharya, Montelionestructure validation
RefinementMethod: simulated annealing / Software ordinal: 1
Details: Structure determination was performed by running CYANA and ASDP in parallel using NOE-based constraints. Consensus peak assignments were selected and used in iterative refinement with CYANA, ...Details: Structure determination was performed by running CYANA and ASDP in parallel using NOE-based constraints. Consensus peak assignments were selected and used in iterative refinement with CYANA, with PHI, PSI and CHI1 dihedral angle constraints from TALOSN, as well as RDC constraints from two alignment media added at later stages. The 20 conformers out of 100 with the lowest target function were further refined by simulated annealing in explicit water bath using the program CNS with PARAM19 force field.
NMR constraintsNOE constraints total: 1702 / NOE intraresidue total count: 435 / NOE long range total count: 512 / NOE medium range total count: 275 / NOE sequential total count: 438 / Hydrogen bond constraints total count: 504 / Protein chi angle constraints total count: 49 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 104 / Protein psi angle constraints total count: 104
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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