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- PDB-3u1n: Structure of the catalytic core of human SAMHD1 -

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Basic information

Entry
Database: PDB / ID: 3u1n
TitleStructure of the catalytic core of human SAMHD1
ComponentsSAM domain and HD domain-containing protein 1
KeywordsHYDROLASE / HD-domain / deoxynucleotide triphosphohydrolase
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
Alpha-Beta Plaits - #2760 / 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. ...Alpha-Beta Plaits - #2760 / 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 / Alpha-Beta Plaits / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.1 Å
AuthorsGoldstone, D.C. / Ennis-Adeniran, V. / Walker, P.A. / Haire, L.F. / Webb, M. / Taylor, I.A.
CitationJournal: Nature / Year: 2011
Title: HIV-1 restriction factor SAMHD1 is a deoxynucleoside triphosphate triphosphohydrolase
Authors: Goldstone, D.C. / Ennis-Adeniran, V. / Hedden, J.J. / Groom, H.C. / Rice, G.I. / Christodoulou, E. / Walker, P.A. / Kelly, G. / Haire, L.F. / Yap, M.W. / de Carvalho, L.P. / Stoye, J.P. / ...Authors: Goldstone, D.C. / Ennis-Adeniran, V. / Hedden, J.J. / Groom, H.C. / Rice, G.I. / Christodoulou, E. / Walker, P.A. / Kelly, G. / Haire, L.F. / Yap, M.W. / de Carvalho, L.P. / Stoye, J.P. / Crow, Y.J. / Taylor, I.A. / Webb, M.
History
DepositionSep 30, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 16, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 14, 2011Group: Database references
Revision 1.2Nov 12, 2014Group: Structure summary
Revision 1.3Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SAM domain and HD domain-containing protein 1
B: SAM domain and HD domain-containing protein 1
C: SAM domain and HD domain-containing protein 1
D: SAM domain and HD domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)246,72812
Polymers246,0864
Non-polymers6428
Water50428
1
A: SAM domain and HD domain-containing protein 1
D: SAM domain and HD domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,3646
Polymers123,0432
Non-polymers3214
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4590 Å2
ΔGint-119 kcal/mol
Surface area34750 Å2
MethodPISA
2
B: SAM domain and HD domain-containing protein 1
C: SAM domain and HD domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,3646
Polymers123,0432
Non-polymers3214
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4590 Å2
ΔGint-119 kcal/mol
Surface area34620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.5160, 95.8180, 96.6610
Angle α, β, γ (deg.)91.1840, 109.2380, 115.2010
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain A and (resseq 118:276 or resseq 284:287 or resseq...A118 - 276
121chain A and (resseq 118:276 or resseq 284:287 or resseq...A284 - 287
131chain A and (resseq 118:276 or resseq 284:287 or resseq...A289 - 311
141chain A and (resseq 118:276 or resseq 284:287 or resseq...A313 - 460
151chain A and (resseq 118:276 or resseq 284:287 or resseq...A468 - 486
161chain A and (resseq 118:276 or resseq 284:287 or resseq...A491 - 504
171chain A and (resseq 118:276 or resseq 284:287 or resseq...A516 - 530
181chain A and (resseq 118:276 or resseq 284:287 or resseq...A548 - 583
211chain B and (resseq 118:276 or resseq 284:287 or resseq...B118 - 276
221chain B and (resseq 118:276 or resseq 284:287 or resseq...B284 - 287
231chain B and (resseq 118:276 or resseq 284:287 or resseq...B289 - 311
241chain B and (resseq 118:276 or resseq 284:287 or resseq...B313 - 460
251chain B and (resseq 118:276 or resseq 284:287 or resseq...B468 - 486
261chain B and (resseq 118:276 or resseq 284:287 or resseq...B491 - 504
271chain B and (resseq 118:276 or resseq 284:287 or resseq...B517 - 531
281chain B and (resseq 118:276 or resseq 284:287 or resseq...B548 - 583
311chain C and (resseq 118:276 or resseq 284:287 or resseq...C118 - 276
321chain C and (resseq 118:276 or resseq 284:287 or resseq...C284 - 287
331chain C and (resseq 118:276 or resseq 284:287 or resseq...C289 - 311
341chain C and (resseq 118:276 or resseq 284:287 or resseq...C313 - 460
351chain C and (resseq 118:276 or resseq 284:287 or resseq...C468 - 486
361chain C and (resseq 118:276 or resseq 284:287 or resseq...C491 - 504
371chain C and (resseq 118:276 or resseq 284:287 or resseq...C517 - 523
381chain C and (resseq 118:276 or resseq 284:287 or resseq...C548 - 583
411chain D and (resseq 118:276 or resseq 284:287 or resseq...D118 - 276
421chain D and (resseq 118:276 or resseq 284:287 or resseq...D284 - 287
431chain D and (resseq 118:276 or resseq 284:287 or resseq...D289 - 311
441chain D and (resseq 118:276 or resseq 284:287 or resseq...D313 - 460
451chain D and (resseq 118:276 or resseq 284:287 or resseq...D468 - 486
461chain D and (resseq 118:276 or resseq 284:287 or resseq...D491 - 504
471chain D and (resseq 118:276 or resseq 284:287 or resseq...D516 - 523
481chain D and (resseq 118:276 or resseq 284:287 or resseq...D548 - 583

NCS oper:
IDCodeMatrixVector
1given(0.999999, 0.000651, -0.001344), (0.000645, -0.999988, -0.004929), (-0.001347, 0.004928, -0.999987)0.05058, 45.090302, 57.124001
2given(-0.982077, -0.072405, -0.174019), (0.09062, 0.628172, -0.77278), (0.165267, -0.774699, -0.610351)-6.16191, 19.2439, 70.285896
3given(-0.981869, 0.07351, 0.174729), (0.091406, -0.623911, 0.776131), (0.166069, 0.77803, 0.60588)-19.403999, 3.00954, 0.56273

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Components

#1: Protein
SAM domain and HD domain-containing protein 1 / Dendritic cell-derived IFNG-induced protein / DCIP / Monocyte protein 5 / MOP-5


Mass: 61521.613 Da / Num. of mol.: 4 / Fragment: unp residues 120-626
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MOP5, SAMHD1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9Y3Z3, Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 28 / 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: 2.57 Å3/Da / Density % sol: 52.23 %
Crystal growMethod: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionRedundancy: 3.7 % / Av σ(I) over netI: 11.63 / Number: 330195 / Rmerge(I) obs: 0.116 / Χ2: 1.05 / D res high: 3.1 Å / D res low: 35 Å / Num. obs: 89495 / % possible obs: 98.7
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
7.083598.410.0640.9873.8
5.637.0899.410.0891.093.8
4.925.6399.310.0881.1073.8
4.474.9299.210.0881.1723.8
4.154.479910.0961.1353.8
3.94.1599.110.1161.1593.8
3.713.998.910.1481.073.8
3.553.7198.810.1931.0143.8
3.413.5598.710.2660.9843.8
3.293.4198.610.3570.9413.6
3.193.2998.210.4720.9453.4
3.13.1996.810.5810.8712.9
ReflectionResolution: 3.1→35 Å / Num. obs: 89495 / % possible obs: 98.7 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.116 / Χ2: 1.047 / Net I/σ(I): 8.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
3.1-3.192.90.58172920.871196.8
3.19-3.293.40.47274670.945198.2
3.29-3.413.60.35774440.941198.6
3.41-3.553.80.26674470.984198.7
3.55-3.713.80.19375361.014198.8
3.71-3.93.80.14874481.07198.9
3.9-4.153.80.11673901.159199.1
4.15-4.473.80.09675051.135199
4.47-4.923.80.08874911.172199.2
4.92-5.633.80.08875351.107199.3
5.63-7.083.80.08974801.09199.4
7.08-353.80.06474600.987198.4

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
SHELXphasing
RESOLVEphasing
PHENIX1.7_650refinement
PDB_EXTRACT3.1data extraction
DENZOdata reduction
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 3.1→34.556 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.39 / σ(F): 0.03 / Phase error: 21.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2275 3760 4.47 %
Rwork0.1959 --
obs0.1973 84061 94.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.807 Å2 / ksol: 0.324 e/Å3
Displacement parametersBiso max: 191.7 Å2 / Biso mean: 63.9185 Å2 / Biso min: 20.23 Å2
Baniso -1Baniso -2Baniso -3
1-3.6253 Å20.8885 Å2-1.2906 Å2
2--0.2978 Å2-5.5467 Å2
3----3.9231 Å2
Refinement stepCycle: LAST / Resolution: 3.1→34.556 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13543 0 24 28 13595
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113893
X-RAY DIFFRACTIONf_angle_d1.20318822
X-RAY DIFFRACTIONf_chiral_restr0.0822038
X-RAY DIFFRACTIONf_plane_restr0.0052438
X-RAY DIFFRACTIONf_dihedral_angle_d16.515006
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A3268X-RAY DIFFRACTIONPOSITIONAL0.032
12B3268X-RAY DIFFRACTIONPOSITIONAL0.032
13C3200X-RAY DIFFRACTIONPOSITIONAL0.058
14D3221X-RAY DIFFRACTIONPOSITIONAL0.054
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.1-3.13920.33451320.33282480261280
3.1392-3.18050.39911060.32242653275984
3.1805-3.2240.30911310.28482717284886
3.224-3.27010.32451330.27312791292488
3.2701-3.31880.2571240.25542821294591
3.3188-3.37070.29211400.23572822296290
3.3707-3.42590.24071370.23372929306691
3.4259-3.48490.2881270.22462911303893
3.4849-3.54820.27361480.20623064321294
3.5482-3.61640.26631550.20512820297595
3.6164-3.69010.27521400.19933080322095
3.6901-3.77020.20631350.18782926306196
3.7702-3.85780.20571380.17873101323996
3.8578-3.95420.21541480.17642997314597
3.9542-4.06090.17821280.16643137326598
4.0609-4.18020.20541600.17293086324698
4.1802-4.31490.20371370.15683062319998
4.3149-4.46880.18751350.15413058319398
4.4688-4.64740.18451560.15693052320898
4.6474-4.85830.17051440.15413161330598
4.8583-5.11370.21351350.16823085322098
5.1137-5.43290.22891540.1783106326098
5.4329-5.85060.2341450.21613096324199
5.8506-6.43590.20521490.2393102325198
6.4359-7.35940.25091360.22453115325199
7.3594-9.24250.22551440.17463076322099
9.2425-34.55860.21071430.20673053319697
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)
12.48011.47130.43770.9252-0.07153.0441-0.05360.05890.2574-0.0263-0.02040.3767-0.3551-0.1679-0.0120.40780.0519-0.04160.26690.07570.343-3.541320.16694.9281
20.9834-0.5581-0.33992.00350.18111.82150.01880.19790.2531-0.2358-0.0196-0.1359-0.43110.1580.00050.371-0.04390.00830.36270.02250.365.522212.86992.0608
30.98010.33880.14630.2301-0.03490.44620.27070.16250.1679-0.1953-0.1988-0.56350.27650.320200.4580.10910.06750.530.04030.456521.4925-9.45460.4648
40.5366-0.07790.19950.0163-0.0560.15640.13391.22150.0836-0.5782-0.1081-0.3964-0.1532-0.0055-0.04311.1265-0.4398-0.10180.6095-0.10250.764416.591632.822618.4189
50.703-0.03980.1430.4274-0.00871.06550.0886-0.3088-0.0957-0.10190.1039-0.36290.28420.519300.26540.07550.00910.56870.02380.481922.1233-9.82438.2224
62.4328-1.1024-0.16530.9325-0.05012.7459-0.0598-0.1285-0.3101-0.0260.04240.44370.4095-0.1838-0.00240.3908-0.05220.03130.25860.03640.3145-3.425324.705852.3422
71.01770.79070.14242.07590.20681.84270.0336-0.1914-0.21170.1986-0.0583-0.09150.40610.19770.00070.32310.045-0.02480.3167-0.00750.33015.494131.985255.161
80.8963-0.2543-0.01340.2806-0.08530.59220.1162-0.1695-0.1066-0.1534-0.0199-0.5634-0.38970.05240.00020.4705-0.1103-0.03480.50250.05830.42421.298154.453956.9623
91.03350.43830.350.66480.09080.13850.2804-0.7406-0.57170.2026-0.0345-0.2078-0.812-0.04670.02431.24890.23620.08560.82360.01190.618316.569912.148338.423
100.46530.3433-0.06570.5948-0.1250.70890.10930.0667-0.0387-0.0760.1099-0.042-0.4350.48580.0070.1775-0.07440.00060.5670.0020.448522.190854.88548.9098
112.0843-0.72091.4091.45570.37072.1123-0.16550.07850.1244-0.073-0.0128-0.0317-0.21610.01410.00010.31430.0309-0.04160.2616-0.02340.3037-13.255451.071238.4663
121.2490.54580.05251.7766-1.61871.8207-0.0124-0.03170.21470.07920.17240.2752-0.4477-0.37310.00040.50880.1432-0.04560.5071-0.03750.5658-21.804254.660637.3496
131.65250.7285-0.21391.516-0.55581.49770.0249-0.25560.11390.07910.03770.50760.0466-0.4842-0.00440.23620.08110.01610.5285-0.00540.4492-27.691540.34453.5172
140.2913-0.28170.01490.23860.00280.0212-0.6237-0.5861-0.2583-0.16430.37290.08430.05740.21570.00091.1987-0.0422-0.20691.1157-0.11160.9061-29.076644.557820.7024
150.40510.0593-0.19940.47130.30180.79810.364-0.2524-0.68080.175-0.06850.12380.8925-0.32040.010.448-0.18060.03480.98980.07880.9099-40.719827.614455.7534
162.16020.5645-1.32081.39280.34951.9013-0.1326-0.07-0.01390.1693-0.0611-0.01440.04290.022-0.00050.2995-0.03450.04060.2434-0.02290.2786-13.3064-6.13918.8642
171.4506-0.75360.30381.9468-1.83352.33570.0052-0.1158-0.09630.18790.19480.33140.3116-0.53420.00380.4286-0.12580.0920.4747-0.0450.4897-22.5283-8.006222.7959
182.1032-0.4690.29591.3256-0.03731.4474-0.03330.43510.0296-0.258-0.01650.40580.0051-0.42060.00010.2716-0.0743-0.05680.56880.02110.4355-27.47194.656-1.0746
190.22750.0617-0.0870.16780.02750.047-0.1320.81370.2359-0.08470.2761-0.1693-0.085-0.2808-0.00051.32310.16070.38221.22640.03910.8776-29.850.813635.7951
200.2624-0.16460.07940.62940.44570.66650.16580.3130.6264-0.65010.11840.1345-1.0263-0.08280.01850.33270.2332-0.16790.89530.01850.8316-40.722817.37181.5853
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 118:216)A118 - 216
2X-RAY DIFFRACTION2(chain A and resid 217:470)A217 - 470
3X-RAY DIFFRACTION3(chain A and resid 471:504)A471 - 504
4X-RAY DIFFRACTION4(chain A and resid 505:530)A505 - 530
5X-RAY DIFFRACTION5(chain A and resid 546:583)A546 - 583
6X-RAY DIFFRACTION6(chain B and resid 118:216)B118 - 216
7X-RAY DIFFRACTION7(chain B and resid 217:470)B217 - 470
8X-RAY DIFFRACTION8(chain B and resid 471:504)B471 - 504
9X-RAY DIFFRACTION9(chain B and resid 505:531)B505 - 531
10X-RAY DIFFRACTION10(chain B and resid 546:583)B546 - 583
11X-RAY DIFFRACTION11(chain C and resid 117:216)C117 - 216
12X-RAY DIFFRACTION12(chain C and resid 217:340)C217 - 340
13X-RAY DIFFRACTION13(chain C and resid 341:504)C341 - 504
14X-RAY DIFFRACTION14(chain C and resid 505:523)C505 - 523
15X-RAY DIFFRACTION15(chain C and resid 547:583)C547 - 583
16X-RAY DIFFRACTION16(chain D and resid 117:216)D117 - 216
17X-RAY DIFFRACTION17(chain D and resid 217:364)D217 - 364
18X-RAY DIFFRACTION18(chain D and resid 365:504)D365 - 504
19X-RAY DIFFRACTION19(chain D and resid 505:523)D505 - 523
20X-RAY DIFFRACTION20(chain D and resid 547:583)D547 - 583

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