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- PDB-4k8o: CRYSTAL STRUCTURE OF THE ATPASE DOMAIN OF TAP1 WITH ATP (D645N, D... -

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Basic information

Entry
Database: PDB / ID: 4k8o
TitleCRYSTAL STRUCTURE OF THE ATPASE DOMAIN OF TAP1 WITH ATP (D645N, D651A MUTANT)
ComponentsAntigen peptide transporter 1
KeywordsTRANSPORT PROTEIN / Nucleotide Binding Domain / Peptide transport
Function / homology
Function and homology information


Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / tapasin binding / ABC-type antigen peptide transporter / ABC-type peptide antigen transporter activity / TAP complex / TAP1 binding / oligopeptide export from mitochondrion / TAP2 binding / peptide antigen transport ...Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / tapasin binding / ABC-type antigen peptide transporter / ABC-type peptide antigen transporter activity / TAP complex / TAP1 binding / oligopeptide export from mitochondrion / TAP2 binding / peptide antigen transport / MHC class Ib protein binding / cytosol to endoplasmic reticulum transport / ABC-type oligopeptide transporter activity / peptide transport / peptide transmembrane transporter activity / MHC class I protein binding / protection from natural killer cell mediated cytotoxicity / MHC class I peptide loading complex / antigen processing and presentation of endogenous peptide antigen via MHC class I / ADP binding / transmembrane transport / defense response / peptide antigen binding / protein transport / adaptive immune response / mitochondrial inner membrane / 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 / CITRIC ACID / NICKEL (II) ION / Antigen peptide transporter 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsVakkasoglu, A.S. / Grossmann, N. / Hulpke, S. / Abele, R. / Tampe, R. / Gaudet, R.
CitationJournal: Nat Commun / Year: 2014
Title: Mechanistic determinants of the directionality and energetics of active export by a heterodimeric ABC transporter.
Authors: Grossmann, N. / Vakkasoglu, A.S. / Hulpke, S. / Abele, R. / Gaudet, R. / Tampe, R.
History
DepositionApr 18, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 3, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 3, 2014Group: Database references

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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)30,2215
Polymers29,4381
Non-polymers7824
Water36020
1
A: Antigen peptide transporter 1
hetero molecules

A: Antigen peptide transporter 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,44110
Polymers58,8772
Non-polymers1,5658
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_557x,-y,-z+21
Buried area4520 Å2
ΔGint-47 kcal/mol
Surface area22410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.260, 123.980, 79.910
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-802-

NI

21A-918-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Antigen peptide transporter 1 / APT1 / ATP-binding cassette sub-family B member 2 / Peptide transporter TAP1


Mass: 29438.436 Da / Num. of mol.: 1 / Fragment: ATPASE DOMAIN, RESIDUES 465-725 / Mutation: D645N, D651A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Abcb2, Mtp1, Tap1, Tap1 Abcb2 Mtp1 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / References: UniProt: P36370

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Non-polymers , 5 types, 24 molecules

#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 2.28 Å3/Da / Density % sol: 46.11 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.85M Sodium tricitrate, 100mM Tris pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 10, 2012
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.65→50 Å / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.65→48.98 Å / SU ML: 0.53 / σ(F): 1.99 / Phase error: 32.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2702 782 10 %
Rwork0.2477 --
obs0.2497 7820 95.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.65→48.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1930 0 46 20 1996
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032014
X-RAY DIFFRACTIONf_angle_d0.7152743
X-RAY DIFFRACTIONf_dihedral_angle_d15.498732
X-RAY DIFFRACTIONf_chiral_restr0.039310
X-RAY DIFFRACTIONf_plane_restr0.002355
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6499-2.81590.42711260.37651138X-RAY DIFFRACTION94
2.8159-3.03330.34791300.3251166X-RAY DIFFRACTION98
3.0333-3.33850.28731320.28371192X-RAY DIFFRACTION99
3.3385-3.82150.28621290.22931157X-RAY DIFFRACTION96
3.8215-4.8140.21521330.20641193X-RAY DIFFRACTION97
4.814-48.98840.25621320.23641192X-RAY DIFFRACTION92
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)
13.8543-0.2566-0.88316.12592.90065.13110.06860.7040.0161-1.398-0.20550.457-0.331-0.41570.10240.62680.0834-0.10820.63260.09330.2879-3.54911.853577.8771
28.0369-3.51121.89278.11385.01217.2692-0.1223-0.3463-0.01260.45420.0616-0.37160.37670.3553-0.01720.3313-0.0558-0.02120.41120.06030.386216.65056.275794.6254
35.52960.18140.02526.11881.23293.5334-0.37-0.05751.2341-0.23820.05980.0154-0.59110.18630.26440.56620.0104-0.07960.38830.09870.55580.986224.749888.2638
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 469 through 563 )
2X-RAY DIFFRACTION2chain 'A' and (resid 564 through 636 )
3X-RAY DIFFRACTION3chain 'A' and (resid 637 through 719 )

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