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- PDB-8s05: ArnAB complex an archaeal ortholog of the Sec23/24 core motif -

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Basic information

Entry
Database: PDB / ID: 8s05
TitleArnAB complex an archaeal ortholog of the Sec23/24 core motif
Components(Conserved protein) x 2
KeywordsPROTEIN BINDING / Sequential Phosphorylation / Archaellum regulatory Network / Trafficking / Sulfolobus acidocaldarius / Sec23/Sec24
Function / homology
Function and homology information


Archaellum regulatory network B, C-terminal / Archaellum regulatory network B, C-terminal domain / Zinc-ribbon domain / zinc-ribbon domain / : / Forkhead associated domain / Forkhead-associated (FHA) domain profile. / FHA domain / Forkhead-associated (FHA) domain / von Willebrand factor type A domain ...Archaellum regulatory network B, C-terminal / Archaellum regulatory network B, C-terminal domain / Zinc-ribbon domain / zinc-ribbon domain / : / Forkhead associated domain / Forkhead-associated (FHA) domain profile. / FHA domain / Forkhead-associated (FHA) domain / von Willebrand factor type A domain / Zinc finger RanBP2 type profile. / Zinc finger RanBP2-type signature. / Zinc finger, RanBP2-type / SMAD/FHA domain superfamily / VWFA domain profile. / von Willebrand factor (vWF) type A domain / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily
Similarity search - Domain/homology
Conserved protein / Conserved protein
Similarity search - Component
Biological speciesSulfolobus acidocaldarius DSM 639 (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 Å
AuthorsKorf, L. / Steinchen, W. / Watad, M. / Bezold, F. / Vogt, M.S. / Selbach, L. / Penner, A. / Tourte, M. / Hepp, S. / Albers, S.V. / Essen, L.-O.
Funding support Germany, 1items
OrganizationGrant numberCountry
Volkswagen FoundationAz-96727 Germany
CitationJournal: To Be Published
Title: Sequential conformational transition of ArnB, an archaeal ortholog with Sec23/Sec24 core motif
Authors: Korf, L. / Steinchen, W. / Watad, M. / Bezold, F. / Vogt, M.S. / Selbach, L. / Penner, A. / Tourte, M. / Hepp, S. / Albers, S.V. / Essen, L.-O.
History
DepositionFeb 13, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 29, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Conserved protein
B: Conserved protein
C: Conserved protein
D: Conserved protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,4878
Polymers137,3104
Non-polymers1774
Water52229
1
A: Conserved protein
C: Conserved protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,7434
Polymers68,6552
Non-polymers882
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Conserved protein
D: Conserved protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,7434
Polymers68,6552
Non-polymers882
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.100, 147.400, 62.640
Angle α, β, γ (deg.)90.00, 107.16, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Conserved protein


Mass: 43672.852 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus acidocaldarius DSM 639 (acidophilic)
Gene: Saci_1211 / Production host: Escherichia coli (E. coli) / References: UniProt: Q4J9H3
#2: Protein Conserved protein


Mass: 24982.027 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus acidocaldarius DSM 639 (acidophilic)
Gene: Saci_1210 / Production host: Escherichia coli (E. coli) / References: UniProt: Q4J9H4
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 29 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 1.61 Å3/Da / Density % sol: 23.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.17 mol/L ammonium acetate, 0.085 mol/L sodium citrate pH 6.0, 25.5% (w/v) PEG 4000, 16.5% (v/v) glycerin

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 29, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.11→49.14 Å / Num. obs: 27478 / % possible obs: 89.9 % / Redundancy: 3.4 % / Biso Wilson estimate: 36.73 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.051 / Rrim(I) all: 0.095 / Net I/σ(I): 9.2
Reflection shellResolution: 2.11→2.36 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.505 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 1375 / CC1/2: 0.638 / Rpim(I) all: 0.416 / Rrim(I) all: 0.659 / % possible all: 52.3

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSMar 15, 2019data reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.11→47.87 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 36.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.264 1364 4.97 %
Rwork0.2082 --
obs0.211 27437 55.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.11→47.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6431 0 4 29 6464
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096536
X-RAY DIFFRACTIONf_angle_d1.0958835
X-RAY DIFFRACTIONf_dihedral_angle_d13.907892
X-RAY DIFFRACTIONf_chiral_restr0.0531033
X-RAY DIFFRACTIONf_plane_restr0.0121130
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.11-2.180.215470.352123X-RAY DIFFRACTION3
2.18-2.270.3859190.3113384X-RAY DIFFRACTION8
2.27-2.370.3244540.29761002X-RAY DIFFRACTION21
2.37-2.50.3243940.30211795X-RAY DIFFRACTION38
2.5-2.660.32061150.30072346X-RAY DIFFRACTION50
2.66-2.860.31141450.28722939X-RAY DIFFRACTION62
2.86-3.150.34091910.25853660X-RAY DIFFRACTION77
3.15-3.60.31242330.2234502X-RAY DIFFRACTION95
3.61-4.540.22462540.17174642X-RAY DIFFRACTION98
4.54-47.870.22722520.17384680X-RAY DIFFRACTION98
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)
11.33060.19590.50462.308-0.74160.8492-0.2606-0.64840.13450.94670.019-0.2317-0.57130.3264-0.3420.18830.02630.07420.1943-0.03330.0332-9.6015-1.8292.3803
21.5767-0.3230.14072.42470.41042.85990.12360.3524-0.1057-0.3295-0.13110.27350.2119-0.2855-0.00440.16070.0528-0.00560.173-0.01790.1426-10.7521-16.3333-24.3563
30.9861-0.9984-0.18952.42250.3461.7409-0.6499-0.6335-0.11281.24880.15630.24740.5571-0.0337-0.11080.21350.0806-0.00020.23420.04080.051-9.5191-8.39634.0098
43.3033-0.75390.6022.4188-0.17881.9108-0.20160.10620.40880.2073-0.03570.2268-0.13980.0053-0.01090.13940.04290.02010.23250.02140.2976-27.20875.1212-6.0533
51.21810.3899-0.22122.18660.68130.3171-0.12770.52030.6057-0.7712-0.30170.0199-0.349-0.4455-0.3030.12370.0804-0.04590.4407-0.03960.3992-24.2352-2.8679-20.1191
60.9444-0.6064-0.15982.35680.12651.7976-0.3156-0.2782-0.13030.33970.09440.06580.10370.4096-0.02070.27950.0446-0.0660.18410.00860.08981.2804-34.76147.6378
72.3279-0.5068-0.71713.1302-1.1631.7198-0.01290.19050.13470.38650.24410.992-0.1811-0.39660.06790.16990.0226-0.02910.19430.02230.28-13.3169-35.46069.8022
81.4707-0.6798-0.92782.72820.03941.9130.0251-0.01950.005-0.0551-0.0628-0.4131-0.19550.19830.02780.08240.062-0.08740.15670.08610.11466.3517-33.564-2.3875
91.2145-0.24740.09961.1682-0.90851.54670.18920.3991-0.098-0.8645-0.1625-0.35240.4025-0.00720.05790.52590.19880.0560.3092-0.00690.2469.377-53.7414-8.2021
100.19710.0241-0.35141.11440.36750.75390.1553-0.1851-0.16870.4646-0.2628-0.1847-0.0280.2819-0.00080.2635-0.0132-0.0540.25380.04480.25081.7247-56.62987.1689
110.18870.22090.04950.26470.07390.0644-0.5966-0.24120.1911-0.3491-0.17620.67660.4632-0.539-0.02240.91210.14220.17560.8521-0.05360.6427-38.99693.80919.6012
120.0841-0.0593-0.23130.10630.25880.7907-0.54120.69090.046-0.2586-0.06750.14720.546-0.3987-0.02140.4678-0.0150.02740.80190.11760.8895-34.20170.64846.103
130.15330.09990.00170.1261-0.02870.10080.3126-0.3443-0.4447-0.29270.21720.3456-0.2907-0.87490.00161.51590.19520.23531.11280.07661.0438.4452-60.3103-22.7373
140.05550.0167-0.14940.10110.01070.5316-0.78390.4129-1.0988-0.8068-0.08520.10930.5366-0.5984-0.00561.35410.1136-0.14950.70650.05011.00636.9615-55.6366-18.5001
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 39 )
2X-RAY DIFFRACTION2chain 'A' and (resid 40 through 210 )
3X-RAY DIFFRACTION3chain 'A' and (resid 211 through 280 )
4X-RAY DIFFRACTION4chain 'A' and (resid 281 through 358 )
5X-RAY DIFFRACTION5chain 'A' and (resid 359 through 382 )
6X-RAY DIFFRACTION6chain 'B' and (resid 3 through 81 )
7X-RAY DIFFRACTION7chain 'B' and (resid 82 through 181 )
8X-RAY DIFFRACTION8chain 'B' and (resid 182 through 280 )
9X-RAY DIFFRACTION9chain 'B' and (resid 281 through 338 )
10X-RAY DIFFRACTION10chain 'B' and (resid 339 through 381 )
11X-RAY DIFFRACTION11chain 'C' and (resid 16 through 25 )
12X-RAY DIFFRACTION12chain 'C' and (resid 26 through 42 )
13X-RAY DIFFRACTION13chain 'D' and (resid 16 through 25 )
14X-RAY DIFFRACTION14chain 'D' and (resid 26 through 41 )

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