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- PDB-2ixg: Crystal structure of the ATPase domain of TAP1 with ATP (S621A, G... -

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Basic information

Entry
Database: PDB / ID: 2ixg
TitleCrystal structure of the ATPase domain of TAP1 with ATP (S621A, G622V, D645N mutant)
ComponentsANTIGEN PEPTIDE TRANSPORTER 1
KeywordsHYDROLASE / ENDOPLASMIC RETICULUM / MEMBRANE / TRANSPORT / ABC ATPASE / ATP- BINDING / PROTEIN TRANSPORT / NUCLEOTIDE-BINDING / TRANSMEMBRANE / IMMUNE RESPONSE / PEPTIDE TRANSPORT
Function / homology
Function and homology information


tapasin binding / ABC-type antigen peptide transporter / ABC-type peptide antigen transporter activity / TAP complex / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / TAP1 binding / peptide antigen transport / TAP2 binding / MHC class Ib protein binding ...tapasin binding / ABC-type antigen peptide transporter / ABC-type peptide antigen transporter activity / TAP complex / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / TAP1 binding / peptide antigen transport / TAP2 binding / MHC class Ib protein binding / cytosol to endoplasmic reticulum transport / peptide transport / peptide transmembrane transporter activity / MHC class I protein binding / protection from natural killer cell mediated cytotoxicity / MHC class I peptide loading complex / transmembrane transport / ADP binding / antigen processing and presentation of endogenous peptide antigen via MHC class I / defense response / peptide antigen binding / protein transport / adaptive immune response / nucleotide binding / protein-containing complex binding / endoplasmic reticulum membrane / 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'-TRIPHOSPHATE / Antigen peptide transporter 1
Similarity search - Component
Biological speciesRATTUS NORVEGICUS (Norway rat)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsProcko, E. / Ferrin-O'Connell, I. / Ng, S.-L. / Gaudet, R.
CitationJournal: Mol.Cell / Year: 2001
Title: Distinct Structural and Functional Properties of the ATPase Sites in an Asymmetric Abc Transporter.
Authors: Procko, E. / Ferrin-O'Connell, I. / Ng, S.-L. / Gaudet, R.
History
DepositionJul 8, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 11, 2006Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2May 8, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.3Dec 13, 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

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Assembly

Deposited unit
A: ANTIGEN PEPTIDE TRANSPORTER 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1083
Polymers29,5091
Non-polymers5992
Water81145
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)67.477, 67.477, 105.903
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein ANTIGEN PEPTIDE TRANSPORTER 1 / TAP1 / APT1 / PEPTIDE TRANSPORTER TAP1 / ATP-BINDING CASSETTE SUB-FAMILY B MEMBER 2


Mass: 29508.521 Da / Num. of mol.: 1 / Fragment: ATPASE DOMAIN, RESIDUES 465-725 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: TRANSPORTER ASSOCIATED WITH ANTIGEN PROCESSING 1 (TAP1)
Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Plasmid: PET21A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P36370
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 45 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, SER 621 TO ALA ENGINEERED RESIDUE IN CHAIN A, GLY 622 TO VAL ...ENGINEERED RESIDUE IN CHAIN A, SER 621 TO ALA ENGINEERED RESIDUE IN CHAIN A, GLY 622 TO VAL ENGINEERED RESIDUE IN CHAIN A, ASP 645 TO ASN
Sequence detailsRESIDUE 464 IS THE START METHIONINE. RESIDUES 726-734 FORM A PURIFICATION TAG

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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: 2.05 Å3/Da / Density % sol: 39.9 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 6
Details: SITTING DROP VAPOR DIFFUSION WITH A RESERVOIR CONTAINING 1.5 M SODIUM MALONATE PH 6.0

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418
DetectorType: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Nov 11, 2005 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→40 Å / Num. obs: 7168 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 4.6 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 11.3
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 3.7 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2IXE

2ixe


Resolution: 2.7→26.47 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.885 / SU B: 28.66 / SU ML: 0.293 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.419 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.267 709 9.9 %RANDOM
Rwork0.212 ---
obs0.217 6424 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.85 Å2
Baniso -1Baniso -2Baniso -3
1-0.28 Å20 Å20 Å2
2--0.28 Å20 Å2
3----0.56 Å2
Refinement stepCycle: LAST / Resolution: 2.7→26.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1931 0 37 45 2013
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0222014
X-RAY DIFFRACTIONr_bond_other_d0.0010.021325
X-RAY DIFFRACTIONr_angle_refined_deg0.791.9922743
X-RAY DIFFRACTIONr_angle_other_deg0.7253.0013239
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.225255
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.01324.11885
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.19315323
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.5611512
X-RAY DIFFRACTIONr_chiral_restr0.0460.2312
X-RAY DIFFRACTIONr_gen_planes_refined0.0010.022237
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02393
X-RAY DIFFRACTIONr_nbd_refined0.1490.2387
X-RAY DIFFRACTIONr_nbd_other0.1550.21380
X-RAY DIFFRACTIONr_nbtor_refined0.1620.2966
X-RAY DIFFRACTIONr_nbtor_other0.0780.21026
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0820.265
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0990.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1480.243
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1790.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.0911.51646
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.10222012
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.1883858
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it0.3134.5730
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.322 56
Rwork0.261 444
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.28080.07420.1352.1362-0.44653.051-0.08990.104-0.0220.0119-0.06690.28030.3683-0.0880.1568-0.1715-0.0469-0.0224-0.06060.0232-0.159847.586821.557347.7778
20.69290.84880.28353.140.121.6109-0.107-0.064-0.0147-0.284-0.0044-0.0250.04830.11270.1115-0.10670.00530.0189-0.07070.0306-0.096149.418827.188545.7067
34.92262.97040.41315.636-2.05253.24280.06240.07520.1678-0.2207-0.00460.21580.0081-0.0945-0.0578-0.04540.0075-0.0073-0.0246-0.0089-0.051771.7535.602250.5736
44.09120.21551.45761.162-0.33553.04610.066-0.0152-0.24470.1638-0.0494-0.25510.34520.1072-0.0167-0.05040.00480.0313-0.09680.0059-0.115759.449315.992458.7006
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A467 - 516
2X-RAY DIFFRACTION2A517 - 562
3X-RAY DIFFRACTION3A563 - 638
4X-RAY DIFFRACTION4A639 - 720

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