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- PDB-1jj7: Crystal Structure of the C-terminal ATPase domain of human TAP1 -

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Basic information

Entry
Database: PDB / ID: 1jj7
TitleCrystal Structure of the C-terminal ATPase domain of human TAP1
ComponentsPEPTIDE TRANSPORTER TAP1
KeywordsPROTEIN TRANSPORT / P-loop / ABC ATPase domain / helical domain
Function / homology
Function and homology information


ABC-type antigen peptide transporter / ABC-type peptide antigen transporter activity / TAP complex / MHC class Ib protein binding / cytosol to endoplasmic reticulum transport / peptide transport / peptide transmembrane transporter activity / TAP1 binding / TAP2 binding / centriolar satellite ...ABC-type antigen peptide transporter / ABC-type peptide antigen transporter activity / TAP complex / MHC class Ib protein binding / cytosol to endoplasmic reticulum transport / peptide transport / peptide transmembrane transporter activity / TAP1 binding / TAP2 binding / centriolar satellite / MHC class I protein binding / endoplasmic reticulum-Golgi intermediate compartment membrane / ADP binding / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / MHC class I peptide loading complex / transmembrane transport / antigen processing and presentation of endogenous peptide antigen via MHC class I / defense response / phagocytic vesicle membrane / peptide antigen binding / protein transport / ER-Phagosome pathway / adaptive immune response / endoplasmic reticulum membrane / endoplasmic reticulum / protein homodimerization activity / ATP hydrolysis activity / ATP binding / membrane / metal ion binding
Similarity search - Function
ABC transporter Tap-like / Type 1 protein exporter / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain ...ABC transporter Tap-like / Type 1 protein exporter / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Antigen peptide transporter 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsGaudet, R. / Wiley, D.C.
CitationJournal: EMBO J. / Year: 2001
Title: Structure of the ABC ATPase domain of human TAP1, the transporter associated with antigen processing.
Authors: Gaudet, R. / Wiley, D.C.
History
DepositionJul 3, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 12, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 1.4Aug 16, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_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_asym_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PEPTIDE TRANSPORTER TAP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5803
Polymers28,1291
Non-polymers4522
Water2,054114
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)87.57, 87.57, 79.85
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number171
Space group name H-MP62
DetailsThe biological assembly is a monomer as contained in the asymmetric unit

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Components

#1: Protein PEPTIDE TRANSPORTER TAP1


Mass: 28128.781 Da / Num. of mol.: 1 / Fragment: C-terminal ABC ATPase domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TAP1 / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q03518
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 114 / Source method: isolated from a natural source / Formula: H2O

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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: 3.14 Å3/Da / Density % sol: 60.83 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 20% PEG8000, 100 mM sodium cacodylate, 200 mM magnesium acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mMTris1drop
250 mM1dropNaCl
310 %glycerol1drop
45 mM1dropMgCl2
51 mMATP1drop
61 mMdithiothreitol1drop
710 mg/mlprotein1drop
820 %PEG80001reservoir
9100 mMsodium cacodylate1reservoir
10200 mMmagnesium acetate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 27, 2000
RadiationMonochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. all: 13714 / Num. obs: 13755 / % possible obs: 99.7 % / Observed criterion σ(F): -1000 / Observed criterion σ(I): -1000 / Redundancy: 3.7 % / Biso Wilson estimate: 52 Å2 / Rmerge(I) obs: 0.053 / Rsym value: 5.3 / Net I/σ(I): 15.9
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.401 / Mean I/σ(I) obs: 3.5 / Num. unique all: 1364 / Rsym value: 40.1 / % possible all: 100
Reflection shell
*PLUS
% possible obs: 100 % / Num. unique obs: 1364

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Processing

Software
NameClassification
CNSrefinement
XDSdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1b0u

1b0u


Resolution: 2.4→30 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.24 1358 -random
Rwork0.198 ---
all0.198 13698 --
obs0.198 13235 96.6 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.85 Å23.22 Å20 Å2
2---1.85 Å20 Å2
3---3.7 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.29 Å0.25 Å
Refinement stepCycle: LAST / Resolution: 2.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1930 0 28 114 2072
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d22.9
X-RAY DIFFRACTIONc_improper_angle_d0.78
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.02
RfactorNum. reflection% reflection
Rfree0.293 219 -
Rwork0.249 --
obs-1859 91.8 %
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 30 Å / σ(F): 0 / Rfactor Rfree: 0.24
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.78
LS refinement shell
*PLUS
Rfactor Rfree: 0.293 / Rfactor Rwork: 0.249

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