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- PDB-5ao1: Crystal structure of human SAMHD1 (amino acid residues 115-583) b... -

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Basic information

Entry
Database: PDB / ID: 5ao1
TitleCrystal structure of human SAMHD1 (amino acid residues 115-583) bound to ddGTP
ComponentsDEOXYNUCLEOSIDE TRIPHOSPHATE TRIPHOSPHOHYDROLASE SAMHD1
KeywordsHYDROLASE / DEOXYNUCLEOSIDE TRIPHOSPHATE TRIPHOSPHOHYDROLASE / HIV RESTRICTION FACTOR
Function / homology
Function and homology information


Nucleotide catabolism / Hydrolases; Acting on ester bonds; Triphosphoric-monoester hydrolases / deoxynucleoside triphosphate hydrolase activity / dGTP binding / triphosphoric monoester hydrolase activity / dATP catabolic process / dGTPase activity / tetraspanin-enriched microdomain / dGTP catabolic process / DNA strand resection involved in replication fork processing ...Nucleotide catabolism / Hydrolases; Acting on ester bonds; Triphosphoric-monoester hydrolases / deoxynucleoside triphosphate hydrolase activity / dGTP binding / triphosphoric monoester hydrolase activity / dATP catabolic process / dGTPase activity / tetraspanin-enriched microdomain / dGTP catabolic process / DNA strand resection involved in replication fork processing / deoxyribonucleotide catabolic process / regulation of innate immune response / negative regulation of type I interferon-mediated signaling pathway / somatic hypermutation of immunoglobulin genes / RNA nuclease activity / double-strand break repair via homologous recombination / Interferon alpha/beta signaling / single-stranded DNA binding / site of double-strand break / protein homotetramerization / defense response to virus / nucleic acid binding / immune response / innate immune response / DNA damage response / GTP binding / RNA binding / zinc ion binding / nucleoplasm / identical protein binding / nucleus / plasma membrane
Similarity search - Function
Hypothetical protein af1432 / Hypothetical protein af1432 / HD domain profile. / HD domain / HD domain / SAM domain (Sterile alpha motif) / SAM domain profile. / Metal dependent phosphohydrolases with conserved 'HD' motif. / Sterile alpha motif. / HD/PDEase domain ...Hypothetical protein af1432 / Hypothetical protein af1432 / HD domain profile. / HD domain / HD domain / SAM domain (Sterile alpha motif) / SAM domain profile. / Metal dependent phosphohydrolases with conserved 'HD' motif. / Sterile alpha motif. / HD/PDEase domain / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
2'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE / : / Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.545 Å
AuthorsSchwefel, D. / Taylor, I.A.
CitationJournal: Plos Pathog. / Year: 2015
Title: Phospho-Dependent Regulation of Samhd1 Oligomerisation Couples Catalysis and Restriction.
Authors: Arnold, L.H. / Groom, H.C.T. / Kunzelmann, S. / Schwefel, D. / Caswell, S.J. / Ordonez, P. / Mann, M.C. / Rueschenbaum, S. / Goldstone, D.C. / Pennell, S. / Howell, S.A. / Stoye, J.P. / ...Authors: Arnold, L.H. / Groom, H.C.T. / Kunzelmann, S. / Schwefel, D. / Caswell, S.J. / Ordonez, P. / Mann, M.C. / Rueschenbaum, S. / Goldstone, D.C. / Pennell, S. / Howell, S.A. / Stoye, J.P. / Webb, M. / Taylor, I.A. / Bishop, K.N.
History
DepositionSep 9, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 14, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: 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_asym_id / _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.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_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_conn.ptnr2_label_seq_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: DEOXYNUCLEOSIDE TRIPHOSPHATE TRIPHOSPHOHYDROLASE SAMHD1
B: DEOXYNUCLEOSIDE TRIPHOSPHATE TRIPHOSPHOHYDROLASE SAMHD1
C: DEOXYNUCLEOSIDE TRIPHOSPHATE TRIPHOSPHOHYDROLASE SAMHD1
D: DEOXYNUCLEOSIDE TRIPHOSPHATE TRIPHOSPHOHYDROLASE SAMHD1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)232,17124
Polymers227,5364
Non-polymers4,63420
Water3,063170
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17830 Å2
ΔGint-164.3 kcal/mol
Surface area67090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.121, 187.356, 81.373
Angle α, β, γ (deg.)90.00, 100.54, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
DEOXYNUCLEOSIDE TRIPHOSPHATE TRIPHOSPHOHYDROLASE SAMHD1 / DNTPASE / DENDRITIC CELL-DERIVED IFNG-INDUCED PROTEIN / DCIP / MONOCYTE PROTEIN 5 / MOP-5 / SAM ...DNTPASE / DENDRITIC CELL-DERIVED IFNG-INDUCED PROTEIN / DCIP / MONOCYTE PROTEIN 5 / MOP-5 / SAM DOMAIN AND HD DOMAIN-CONTAINING PROTEIN 1 / SAMHD1


Mass: 56884.098 Da / Num. of mol.: 4 / Fragment: UNP RESIDUES 115-583
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA2
References: UniProt: Q9Y3Z3, Hydrolases; Acting on ester bonds; Triphosphoric-monoester hydrolases

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Non-polymers , 5 types, 190 molecules

#2: Chemical
ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#3: Chemical
ChemComp-DG3 / 2'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE


Mass: 491.182 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H16N5O12P3
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 170 / 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: 2.41 Å3/Da / Density % sol: 49.1 % / Description: NONE
Crystal growDetails: 100 MM BIS TRIS PROPANE-HCL, 150 MM NA2SO4, 13.5% PEG 3350 PH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 1.735
DetectorType: DECTRIS PILATUS / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.735 Å / Relative weight: 1
ReflectionResolution: 2.54→50 Å / Num. obs: 65199 / % possible obs: 96.6 % / Observed criterion σ(I): -3 / Redundancy: 6.26 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 17.96
Reflection shellResolution: 2.54→2.7 Å / Redundancy: 4.12 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 1.61 / % possible all: 80

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.9_1692)refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3U1N

3u1n


Resolution: 2.545→49.228 Å / SU ML: 0.33 / σ(F): 2 / Phase error: 25.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2201 3290 5.1 %
Rwork0.1709 --
obs0.1734 65181 96.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.545→49.228 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14132 0 268 170 14570
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01115370
X-RAY DIFFRACTIONf_angle_d1.53220796
X-RAY DIFFRACTIONf_dihedral_angle_d18.2385837
X-RAY DIFFRACTIONf_chiral_restr0.0672179
X-RAY DIFFRACTIONf_plane_restr0.0092648
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5448-2.58270.336800.31681455X-RAY DIFFRACTION53
2.5827-2.62310.35631290.27222360X-RAY DIFFRACTION85
2.6231-2.66610.32311240.25442549X-RAY DIFFRACTION92
2.6661-2.71210.31941320.2392675X-RAY DIFFRACTION95
2.7121-2.76140.28941410.2292693X-RAY DIFFRACTION100
2.7614-2.81450.2851610.22342816X-RAY DIFFRACTION100
2.8145-2.87190.30281610.23592730X-RAY DIFFRACTION100
2.8719-2.93440.32691380.23842809X-RAY DIFFRACTION100
2.9344-3.00260.2591290.22072789X-RAY DIFFRACTION100
3.0026-3.07770.29651380.22352779X-RAY DIFFRACTION100
3.0777-3.16090.28641650.21962774X-RAY DIFFRACTION100
3.1609-3.25390.27731600.20742778X-RAY DIFFRACTION100
3.2539-3.35890.28421590.20152777X-RAY DIFFRACTION100
3.3589-3.47890.24841480.18852761X-RAY DIFFRACTION100
3.4789-3.61820.21631470.17762773X-RAY DIFFRACTION100
3.6182-3.78280.20841330.16262796X-RAY DIFFRACTION100
3.7828-3.98210.20711400.14632792X-RAY DIFFRACTION100
3.9821-4.23150.16951330.1372809X-RAY DIFFRACTION100
4.2315-4.5580.15821610.13222765X-RAY DIFFRACTION100
4.558-5.01630.17341550.1282803X-RAY DIFFRACTION100
5.0163-5.74120.20341380.14192794X-RAY DIFFRACTION100
5.7412-7.22960.18211630.16492784X-RAY DIFFRACTION100
7.2296-49.23750.18651550.13992830X-RAY DIFFRACTION100
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)
11.1335-0.1056-0.09920.78160.01311.8295-0.00120.162-0.02-0.17210.11210.17450.1934-0.7091-0.09520.2797-0.0758-0.08160.49640.07080.3423-4.0905-23.27420.7379
21.86230.0796-0.20930.8244-0.24010.83510.12430.47970.1279-0.38720.09130.2059-0.1854-0.4416-0.13120.4750.0584-0.05160.54780.10580.39640.1606-10.336810.4658
30.6233-0.1047-0.07420.47870.04931.59370.02240.0674-0.15640.01150.0689-0.00180.81550.1393-0.05260.58490.0696-0.0260.2271-0.01690.290215.2099-38.14618.7925
41.35120.2454-0.43241.6625-0.01721.1961-0.07530.23960.1836-0.19630.1335-0.14810.4190.0247-0.05480.74760.1507-0.06280.5347-0.06760.347621.8625-34.40352.4188
50.1866-0.04190.02890.20050.17250.2292-0.07270.55320.1445-0.82370.77890.3618-0.1428-0.1349-0.08170.97120.1006-0.07220.68660.15120.78143.656-3.37952.4554
61.17180.6729-0.29950.80180.04840.8661-0.13410.4207-0.4071-0.0930.24850.01780.3470.6787-0.05510.59490.24430.04750.7392-0.14450.399830.6821-32.45313.0569
71.4094-0.1757-0.35971.0699-0.05012.94010.1861-0.0729-0.03550.03430.0247-0.18830.43950.8221-0.07440.18010.0856-0.03930.3512-0.05810.253627.1944-24.368240.8541
80.926-0.91131.00671.6669-0.97781.0116-0.1478-0.92790.37010.98680.1322-0.5709-0.37970.4479-0.00880.3415-0.066-0.0911.0857-0.1430.418934.032-17.20455.136
90.1499-0.0802-0.16720.0472-0.01381.43050.3384-0.19950.3150.0161-0.11540.0117-0.47270.29130.01560.3345-0.07830.06680.3707-0.04920.462722.5092-7.514942.1494
103.28211.03110.49910.47080.40110.71520.1679-0.76490.41750.72520.2006-0.0537-0.23490.5044-0.0870.5922-0.11650.11730.4508-0.1780.535921.1535-4.217249.9531
111.2056-0.1443-0.52330.9862-0.72772.2973-0.013-0.0578-0.1849-0.02710.11560.180.9191-0.2754-0.03060.5034-0.0983-0.05650.24150.01840.34465.715-34.781445.2881
120.19260.4734-0.04271.99150.2572.1442-0.2497-0.471-0.19740.39660.30470.22840.5111-0.7607-0.05470.4152-0.19010.01080.71370.11810.4057-5.6607-32.034463.2708
131.0588-0.183-0.69950.7248-0.14151.28640.2176-0.1119-0.07050.16530.288-0.4978-0.27710.0794-0.19470.3859-0.10260.07240.5607-0.00950.493112.0059-14.357455.0356
141.7474-1.31391.05421.0356-1.0242.2398-0.1052-0.4378-0.04820.26720.04060.2838-0.1729-1.01540.01480.426-0.07980.0860.90650.18130.521-9.3521-23.101462.7423
150.66420.3039-0.23950.79920.2311.6963-0.0260.05960.0478-0.16980.126-0.1209-0.19330.5393-0.04770.3462-0.11090.06890.4487-0.020.306524.063224.374124.5169
162.01940.173-0.57310.6001-0.28580.53290.04630.06720.1132-0.5060.0035-0.1336-0.06820.3718-0.02780.5633-0.09070.12630.6168-0.07460.424326.770320.295413.9899
171.6198-0.5277-0.23520.973-0.31211.4677-0.08620.11480.0962-0.14890.08620.184-0.21650.1092-0.00460.4477-0.0505-0.0330.29540.03930.294711.746827.675620.5799
180.58620.08480.21360.0879-0.18580.4728-0.39130.4852-0.1587-0.32210.33320.149-0.3088-0.14560.00910.8423-0.0563-0.10170.61590.07930.5049-0.264736.1398.1006
19-0.0972-0.1255-0.10970.4217-0.24310.3480.0830.56210.2478-0.4562-0.18610.00790.1664-0.15430.04240.81010.0291-0.12910.62650.0090.6462.669229.91035.9304
200.8129-0.91590.270.975-0.3340.105-0.12070.32-0.1249-0.41190.19540.24210.10590.0304-0.05610.90.0116-0.07990.58570.00560.55948.132217.4986.2354
210.73170.7674-0.17830.9243-0.18360.2448-0.03540.61290.3272-0.99140.57120.2901-0.6134-0.37680.00361.0034-0.0758-0.36420.89520.27710.6194-11.073736.04314.3677
221.0118-0.2218-0.03150.9639-0.03221.70690.09990.0193-0.0412-0.06970.0130.2387-0.1347-0.2695-0.06610.2312-0.00770.01220.20880.03510.3272-3.788221.670142.1868
231.3332-0.1796-0.04020.68410.44311.12220.0883-0.16280.02720.1707-0.10610.1861-0.1102-0.5738-0.02480.30330.00260.05680.49130.02050.4928-10.874520.755449.3524
241.80150.38260.25791.0118-0.31351.75380.0289-0.1726-0.12350.0820.06880.0329-0.0717-0.0865-0.07340.2855-0.03350.04040.20770.04010.21744.708420.645147.6013
250.8157-0.01620.13950.98-0.19541.40880.0371-0.31830.06070.0920.1138-0.0442-0.04780.3261-0.0940.4606-0.16880.01880.519-0.00050.352421.602825.402658.4733
260.2239-0.42260.25311.2096-0.25661.27340.2409-0.3811-0.08950.27270.04030.14940.06790.0317-0.16170.3859-0.1313-0.0370.58270.09410.299117.863514.292760.246
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 115 THROUGH 273 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 274 THROUGH 372 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 373 THROUGH 469 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 470 THROUGH 514 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 515 THROUGH 547 )
6X-RAY DIFFRACTION6CHAIN 'A' AND (RESID 548 THROUGH 583 )
7X-RAY DIFFRACTION7CHAIN 'B' AND (RESID 115 THROUGH 273 )
8X-RAY DIFFRACTION8CHAIN 'B' AND (RESID 274 THROUGH 309 )
9X-RAY DIFFRACTION9CHAIN 'B' AND (RESID 310 THROUGH 343 )
10X-RAY DIFFRACTION10CHAIN 'B' AND (RESID 344 THROUGH 372 )
11X-RAY DIFFRACTION11CHAIN 'B' AND (RESID 373 THROUGH 469 )
12X-RAY DIFFRACTION12CHAIN 'B' AND (RESID 470 THROUGH 494 )
13X-RAY DIFFRACTION13CHAIN 'B' AND (RESID 495 THROUGH 558 )
14X-RAY DIFFRACTION14CHAIN 'B' AND (RESID 559 THROUGH 583 )
15X-RAY DIFFRACTION15CHAIN 'C' AND (RESID 115 THROUGH 260 )
16X-RAY DIFFRACTION16CHAIN 'C' AND (RESID 261 THROUGH 323 )
17X-RAY DIFFRACTION17CHAIN 'C' AND (RESID 324 THROUGH 450 )
18X-RAY DIFFRACTION18CHAIN 'C' AND (RESID 451 THROUGH 481 )
19X-RAY DIFFRACTION19CHAIN 'C' AND (RESID 482 THROUGH 522 )
20X-RAY DIFFRACTION20CHAIN 'C' AND (RESID 523 THROUGH 558 )
21X-RAY DIFFRACTION21CHAIN 'C' AND (RESID 559 THROUGH 583 )
22X-RAY DIFFRACTION22CHAIN 'D' AND (RESID 113 THROUGH 232 )
23X-RAY DIFFRACTION23CHAIN 'D' AND (RESID 233 THROUGH 323 )
24X-RAY DIFFRACTION24CHAIN 'D' AND (RESID 324 THROUGH 435 )
25X-RAY DIFFRACTION25CHAIN 'D' AND (RESID 436 THROUGH 517 )
26X-RAY DIFFRACTION26CHAIN 'D' AND (RESID 518 THROUGH 582 )

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  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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