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- PDB-5zxd: Crystal structure of ATP-bound human ABCF1 -

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Basic information

Entry
Database: PDB / ID: 5zxd
TitleCrystal structure of ATP-bound human ABCF1
ComponentsATP-binding cassette sub-family F member 1
KeywordsTRANSLATION / Regulator
Function / homology
Function and homology information


: / translation activator activity / translation factor activity, RNA binding / translational initiation / positive regulation of translation / ABC-family proteins mediated transport / transmembrane transport / ribosome binding / nuclear envelope / inflammatory response ...: / translation activator activity / translation factor activity, RNA binding / translational initiation / positive regulation of translation / ABC-family proteins mediated transport / transmembrane transport / ribosome binding / nuclear envelope / inflammatory response / translation / ATP hydrolysis activity / RNA binding / nucleoplasm / ATP binding / membrane / cytoplasm / cytosol
Similarity search - Function
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. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / ATP-binding cassette sub-family F member 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.288 Å
AuthorsQu, L. / Jiang, Y. / Liu, Z.J.
Funding support China, 6items
OrganizationGrant numberCountry
Ministry of Science and Technology (China)2014CB910400 China
Ministry of Science and Technology (China)2015CB910104 China
National Natural Science Foundation of China31330019 China
National Natural Science Foundation of China31770948 China
National Natural Science Foundation of China31570875 China
National Natural Science Foundation of China81590761 China
CitationJournal: Structure / Year: 2018
Title: Crystal Structure of ATP-Bound Human ABCF1 Demonstrates a Unique Conformation of ABC Proteins
Authors: Qu, L. / Jiang, Y. / Cheng, C. / Wu, D. / Meng, B. / Chen, Z. / Zhu, Y. / Shaw, N. / Ouyang, S. / Liu, Z.J.
History
DepositionMay 18, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 25, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 1, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed
Revision 1.2Sep 19, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ATP-binding cassette sub-family F member 1
B: ATP-binding cassette sub-family F member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,1686
Polymers125,1402
Non-polymers2,0294
Water5,567309
1
A: ATP-binding cassette sub-family F member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,5843
Polymers62,5701
Non-polymers1,0142
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area600 Å2
ΔGint-2 kcal/mol
Surface area23010 Å2
MethodPISA
2
B: ATP-binding cassette sub-family F member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,5843
Polymers62,5701
Non-polymers1,0142
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1220 Å2
ΔGint-7 kcal/mol
Surface area24380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.068, 132.814, 148.329
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein ATP-binding cassette sub-family F member 1 / ATP-binding cassette 50 / TNF-alpha-stimulated ABC protein


Mass: 62569.863 Da / Num. of mol.: 2 / Fragment: UNP residues 300-841
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ABCF1, ABC50
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q8NE71
#2: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 309 / 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: 2.6 Å3/Da / Density % sol: 52.7 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop
Details: potassium thiocyanate, PEG 3350, sodium citrate, glycerol

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9754 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 17, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9754 Å / Relative weight: 1
ReflectionResolution: 2.288→42.42 Å / Num. obs: 58677 / % possible obs: 98.28 % / Redundancy: 12.6 % / Biso Wilson estimate: 36.16 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.1164 / Rpim(I) all: 0.03388 / Rrim(I) all: 0.1214 / Net I/σ(I): 17.05
Reflection shellResolution: 2.288→2.37 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.8338 / Num. unique obs: 4857 / CC1/2: 0.75 / Rpim(I) all: 0.3073 / Rrim(I) all: 0.8937 / % possible all: 82.93

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Processing

Software
NameVersionClassification
PHENIX1.13-2998refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.288→42.42 Å / Cross valid method: FREE R-VALUE / Phase error: 22.78
RfactorNum. reflection% reflection
Rfree0.2241 2003 3.4 %
Rwork0.1937 --
obs0.1947 58666 98.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 47.98 Å2
Refinement stepCycle: LAST / Resolution: 2.288→42.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7571 0 124 309 8004
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONBOND0.003
X-RAY DIFFRACTIONANGLE0.726
X-RAY DIFFRACTIONCHIRALITY0.045
X-RAY DIFFRACTIONPLANARITY0.004
X-RAY DIFFRACTIONDIHEDRAL8.33
LS refinement shellResolution: 2.288→2.37 Å
RfactorNum. reflection% reflection
Rfree0.3245 -3.4 %
Rwork0.2997 4854 -
obs--82.93 %
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.4049-0.20110.30273.06990.42070.9365-0.255-0.45560.01380.65210.2290.2446-0.1414-0.28070.0340.40770.17030.01780.47130.03460.2682-19.9118103.660328.4859
20.10740.13510.09850.77250.65250.52710.0620.1113-0.17560.0359-0.10650.06520.4513-0.03610.04240.344-0.06110.04270.3604-0.0550.4412-22.509382.37333.7899
31.70110.27430.41663.7422-0.10474.0387-0.07490.09660.42120.02490.0228-0.1867-0.4613-0.02250.0910.1583-0.0268-0.02960.2481-0.00460.3686-15.877127.10841.0196
43.94310.89621.0481.36440.25441.5334-0.1273-0.15060.1019-0.07660.00990.191-0.0834-0.15670.09850.1874-0.0041-0.0140.22620.00110.2478-29.7383107.3628-0.2707
51.511-0.02160.10642.80960.63642.4364-0.1753-0.16050.10950.35450.2178-0.5615-0.09290.447-0.03850.23930.0404-0.0580.3411-0.03110.409-6.2249114.776210.8064
61.76242.0560.74394.28752.64523.8747-0.11310.12290.2169-0.359-0.01320.39550.1457-0.62640.16840.4187-0.1297-0.03030.46350.12850.3583-26.598865.278447.5835
74.77612.1037-3.00172.6388-1.19383.46430.2139-0.05790.49670.00670.02770.34-0.3402-0.0949-0.2490.3534-0.00980.01680.30.05180.4053-22.986777.499565.5987
82.91181.08241.27732.1792.26765.1748-0.02950.2751-0.18470.01070.0597-0.0340.7969-0.0834-0.05760.4917-0.07340.01660.35220.12130.3398-12.644859.640647.1433
92.10090.6485-0.13865.55290.26633.17330.0291-0.12270.04460.35240.0035-0.006-0.27390.3754-0.00570.32910.0255-0.01710.26290.08880.18485.400979.264334.9561
100.64731.0342-0.95033.12850.34793.6885-0.0611-0.15420.2257-0.03150.12750.5769-0.5467-0.1224-0.02260.51580.0716-0.05450.3690.14950.4222-0.24283.879127.5117
116.7430.67772.41262.21510.59735.5031-0.07420.1539-0.083-0.10070.10330.25220.1187-0.2085-0.01130.28080.00470.00630.19030.05610.2641-7.090869.122324.0722
122.46960.5051-2.150.1117-0.68916.12250.0084-0.2337-0.06830.003-0.03920.0329-0.10410.36540.07320.32860.0168-0.04360.30450.09160.33064.090571.037549.2389
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 234 )A2 - 234
2X-RAY DIFFRACTION2chain 'A' and (resid 235 through 320 )A235 - 320
3X-RAY DIFFRACTION3chain 'A' and (resid 321 through 391 )A321 - 391
4X-RAY DIFFRACTION4chain 'A' and (resid 392 through 489 )A392 - 489
5X-RAY DIFFRACTION5chain 'A' and (resid 490 through 542 )A490 - 542
6X-RAY DIFFRACTION6chain 'B' and (resid 3 through 84 )B3 - 84
7X-RAY DIFFRACTION7chain 'B' and (resid 85 through 170 )B85 - 170
8X-RAY DIFFRACTION8chain 'B' and (resid 171 through 251 )B171 - 251
9X-RAY DIFFRACTION9chain 'B' and (resid 252 through 374 )B252 - 374
10X-RAY DIFFRACTION10chain 'B' and (resid 375 through 408 )B375 - 408
11X-RAY DIFFRACTION11chain 'B' and (resid 409 through 489 )B409 - 489
12X-RAY DIFFRACTION12chain 'B' and (resid 490 through 547 )B490 - 547

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