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- PDB-2ixe: Crystal structure of the ATPase domain of TAP1 with ATP (D645N mutant) -

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Basic information

Entry
Database: PDB / ID: 2ixe
TitleCrystal structure of the ATPase domain of TAP1 with ATP (D645N mutant)
ComponentsANTIGEN PEPTIDE TRANSPORTER 1
KeywordsHYDROLASE / ABC ATPASE
Function / homology
Function and homology information


Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / tapasin binding / ABC-type peptide antigen transporter activity / ABC-type antigen peptide transporter / TAP complex / TAP2 binding / TAP1 binding / peptide antigen transport / MHC class Ib protein binding ...Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / tapasin binding / ABC-type peptide antigen transporter activity / ABC-type antigen peptide transporter / TAP complex / TAP2 binding / TAP1 binding / peptide antigen transport / 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 / defense response / antigen processing and presentation of endogenous peptide antigen via MHC class I / ADP binding / peptide antigen binding / transmembrane transport / protein transport / adaptive immune response / nucleotide binding / endoplasmic reticulum membrane / protein-containing complex binding / protein homodimerization activity / ATP hydrolysis activity / ATP binding / metal ion binding / membrane
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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / PHOSPHATE ION / Antigen peptide transporter 1
Similarity search - Component
Biological speciesRATTUS NORVEGICUS (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 7, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 11, 2006Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2May 8, 2019Group: Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.3May 15, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Dec 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 / pdbx_struct_conn_angle / 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 / _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.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.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.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_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

Downloads & links

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Assembly

Deposited unit
A: ANTIGEN PEPTIDE TRANSPORTER 1
D: ANTIGEN PEPTIDE TRANSPORTER 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,1237
Polymers58,9652
Non-polymers1,1585
Water5,981332
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4210 Å2
ΔGint-34.1 kcal/mol
Surface area20950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.431, 80.431, 168.115
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.99721, -0.01671, 0.07271), (-0.02659, -0.83104, -0.55557), (0.06971, -0.55596, 0.82828)
Vector: -44.13889, 24.91733, 8.85256)

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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: 29482.443 Da / Num. of mol.: 2 / 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


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 332 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, ASP 645 TO ASN ENGINEERED RESIDUE IN CHAIN D, ASP 645 TO ASN
Sequence detailsRESIDUE 464 IS THE START METHIONINE.

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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: 2.31 Å3/Da / Density % sol: 46.7 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: HANGING DROP VAPOR DIFFUSION AT 4C WITH A RESERVOIR CONTAING 1.0 M POTASSIUM PHOSPHATE PH 8.0

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794
DetectorType: ADSC CCD / Detector: CCD / Date: Aug 17, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 38086 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 9 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 26.6
Reflection shellResolution: 2→2.09 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 3 / % possible all: 97.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1JJ7

1jj7


Resolution: 2→72.55 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.93 / SU B: 8.288 / SU ML: 0.127 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.195 / ESU R Free: 0.171 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.241 2705 7.1 %RANDOM
Rwork0.199 ---
obs0.202 35301 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.27 Å2
Baniso -1Baniso -2Baniso -3
1-0.29 Å20 Å20 Å2
2--0.29 Å20 Å2
3----0.58 Å2
Refinement stepCycle: LAST / Resolution: 2→72.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3767 0 69 332 4168
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0213953
X-RAY DIFFRACTIONr_bond_other_d0.0010.023607
X-RAY DIFFRACTIONr_angle_refined_deg1.0941.9865399
X-RAY DIFFRACTIONr_angle_other_deg0.73538364
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1685509
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.07323.892167
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.56715618
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4021525
X-RAY DIFFRACTIONr_chiral_restr0.060.2619
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024419
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02782
X-RAY DIFFRACTIONr_nbd_refined0.1890.2813
X-RAY DIFFRACTIONr_nbd_other0.1630.23586
X-RAY DIFFRACTIONr_nbtor_refined0.1720.21888
X-RAY DIFFRACTIONr_nbtor_other0.080.22358
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1270.2284
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.180.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.20.264
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1390.219
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5531.53221
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.6423972
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.06131666
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.614.51420
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→2.05 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.286 160
Rwork0.237 2520
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)
17.2971.49280.32343.88730.20122.66240.11810.3978-0.04620.024-0.0489-0.26450.06130.2079-0.0692-0.1805-0.1065-0.0468-0.0374-0.0161-0.3466-0.91222.041-5.653
24.81112.71141.14973.89291.47941.7977-0.1580.9422-0.194-0.27910.3224-0.3401-0.05520.3745-0.1644-0.1274-0.128-0.01230.1725-0.0129-0.2575-0.67619.324-12.641
35.11131.3805-0.88662.81750.05866.78810.14810.1027-0.231-0.04310.0368-0.09770.4434-0.2428-0.185-0.1-0.0493-0.0493-0.1380.0056-0.2357-16.8842.074-18.496
46.38273.76620.15863.67130.26412.76740.2564-0.3491-0.88220.4001-0.1948-0.51250.17780.4602-0.0616-0.0976-0.0275-0.08640.01910.07-0.1463-11.5847.265-2.829
56.8043.212-0.61129.927-6.3527.56060.4783-1.34650.02421.0547-0.15250.0032-0.1026-0.3773-0.32580.0561-0.2246-0.0670.25170.0139-0.3156-8.57918.8519.512
62.098-0.29180.18872.06430.15322.27770.03490.125-0.1136-0.1403-0.07760.14020.0483-0.11940.0427-0.1949-0.02630.0189-0.23970.0068-0.3197-44.30410.041-8.543
71.3168-1.29890.24342.91970.21111.89470.05490.25040.1345-0.2053-0.09520.0469-0.1664-0.10840.0403-0.1782-0.00520.0104-0.17650.0241-0.2929-45.7115.896-12.404
812.6260.6629-0.64886.9992-1.20194.30360.67870.31971.31610.5334-0.4197-0.3298-0.920.5006-0.25910.2639-0.18070.1062-0.01720.06180.0548-29.11334.115-8.358
94.87821.3022-1.67631.53080.28864.42610.1371-0.45370.19420.0766-0.074-0.1678-0.27350.3883-0.0631-0.1609-0.05630.0067-0.1414-0.019-0.2695-33.42420.9141.922
102.56080.00911.79021.5184-0.11468.91080.0825-0.2708-0.34410.1999-0.0163-0.34750.71810.494-0.0662-0.0990.0029-0.0005-0.13210.0618-0.2385-34.7083.6065.999
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A470 - 519
2X-RAY DIFFRACTION2A520 - 564
3X-RAY DIFFRACTION3A565 - 638
4X-RAY DIFFRACTION4A639 - 683
5X-RAY DIFFRACTION5A684 - 719
6X-RAY DIFFRACTION6D467 - 519
7X-RAY DIFFRACTION7D520 - 562
8X-RAY DIFFRACTION8D565 - 638
9X-RAY DIFFRACTION9D639 - 683
10X-RAY DIFFRACTION10D684 - 721

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