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- PDB-8vy5: Crystal structure of human SAE1 -

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Basic information

Entry
Database: PDB / ID: 8vy5
TitleCrystal structure of human SAE1
ComponentsSUMO-activating enzyme subunit 1, N-terminally processed
KeywordsONCOPROTEIN / SAE1 / sumoylation / SUMO1 activating enzyme subunit 1 / Cancer
Function / homology
Function and homology information


SUMO activating enzyme complex / ubiquitin activating enzyme activity / SUMO is conjugated to E1 (UBA2:SAE1) / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / positive regulation of protein sumoylation / small protein activating enzyme binding / ATP-dependent protein binding / positive regulation of protein targeting to mitochondrion / protein sumoylation / enzyme activator activity ...SUMO activating enzyme complex / ubiquitin activating enzyme activity / SUMO is conjugated to E1 (UBA2:SAE1) / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / positive regulation of protein sumoylation / small protein activating enzyme binding / ATP-dependent protein binding / positive regulation of protein targeting to mitochondrion / protein sumoylation / enzyme activator activity / protein heterodimerization activity / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Ubiquitin/SUMO-activating enzyme E1-like / ThiF/MoeB/HesA family / THIF-type NAD/FAD binding fold / ThiF family / Ubiquitin-activating enzyme
Similarity search - Domain/homology
SUMO-activating enzyme subunit 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 Å
AuthorsHuang, X. / Qian, J. / Yang, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Crystal structure of human SAE1
Authors: Yang, Y.
History
DepositionFeb 7, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 19, 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: SUMO-activating enzyme subunit 1, N-terminally processed
B: SUMO-activating enzyme subunit 1, N-terminally processed


Theoretical massNumber of molelcules
Total (without water)71,2512
Polymers71,2512
Non-polymers00
Water1,54986
1
A: SUMO-activating enzyme subunit 1, N-terminally processed


Theoretical massNumber of molelcules
Total (without water)35,6261
Polymers35,6261
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: SUMO-activating enzyme subunit 1, N-terminally processed


Theoretical massNumber of molelcules
Total (without water)35,6261
Polymers35,6261
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)103.197, 70.187, 87.591
Angle α, β, γ (deg.)90.000, 108.920, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 30 through 31 or resid 33...
d_2ens_1(chain "B" and (resid 30 through 31 or resid 33...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ALAALAGLNGLNAA30 - 3127 - 28
d_12ARGARGLEULEUAA33 - 3430 - 31
d_13ALAALASERSERAA36 - 3733 - 34
d_14VALVALILEILEAA39 - 8236 - 79
d_15THRTHRGLUGLUAA84 - 11681 - 113
d_16LYSLYSPROPROAA118 - 119115 - 116
d_17SERSERGLUGLUAA121 - 173118 - 170
d_18VALVALLEULEUAA211 - 220185 - 194
d_19VALVALVALVALAA222196
d_110THRTHRVALVALAA237 - 276211 - 250
d_111ASPASPGLYGLYAA278 - 333252 - 307
d_112GLYGLYLEULEUAA336 - 343310 - 317
d_21ALAALAGLNGLNBB30 - 3127 - 28
d_22ARGARGLEULEUBB33 - 3430 - 31
d_23ALAALASERSERBB36 - 3733 - 34
d_24VALVALILEILEBB39 - 8236 - 79
d_25THRTHRGLUGLUBB84 - 11681 - 113
d_26LYSLYSPROPROBB118 - 119115 - 116
d_27SERSERLEULEUBB121 - 220118 - 194
d_28VALVALVALVALBB222196
d_29THRTHRVALVALBB237 - 276211 - 250
d_210ASPASPGLYGLYBB278 - 333252 - 307
d_211GLYGLYLEULEUBB336 - 343310 - 317

NCS oper: (Code: givenMatrix: (-0.983246713525, 0.0861559686183, -0.16063327617), (0.076083555077, -0.606826145273, -0.791184758486), (-0.165641761004, -0.790151364287, 0.590104760637)Vector: 45. ...NCS oper: (Code: given
Matrix: (-0.983246713525, 0.0861559686183, -0.16063327617), (0.076083555077, -0.606826145273, -0.791184758486), (-0.165641761004, -0.790151364287, 0.590104760637)
Vector: 45.3463373697, 10.468627346, 9.67206079448)

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Components

#1: Protein SUMO-activating enzyme subunit 1, N-terminally processed


Mass: 35625.598 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SAE1, AOS1, SUA1, UBLE1A / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UBE0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / Source method: isolated from a natural source / Formula: H2O
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: 2.13 Å3/Da / Density % sol: 42.25 %
Crystal growTemperature: 291 K / Method: evaporation / Details: Tris 8.5, PEG3350, ammonium acetate NDSB-256

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.97918 Å
DetectorType: MAR CCD 300 mm / Detector: CCD / Date: Mar 21, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.01→56.99 Å / Num. obs: 38233 / % possible obs: 96.4 % / Redundancy: 6.1 % / Biso Wilson estimate: 45.11 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.035 / Rrim(I) all: 0.064 / Rsym value: 0.058 / Net I/σ(I): 13.2
Reflection shellResolution: 2.01→2.12 Å / Rmerge(I) obs: 1.141 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 5741 / CC1/2: 0.482 / Rpim(I) all: 0.918 / Rsym value: 1.325

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
XDSdata scaling
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.01→28.29 Å / SU ML: 0.2798 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.1337
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.274 1897 5.01 %
Rwork0.2306 35988 -
obs0.2327 37885 95.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 69.13 Å2
Refinement stepCycle: LAST / Resolution: 2.01→28.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4350 0 0 86 4436
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00664425
X-RAY DIFFRACTIONf_angle_d1.23145971
X-RAY DIFFRACTIONf_chiral_restr0.0494678
X-RAY DIFFRACTIONf_plane_restr0.0239781
X-RAY DIFFRACTIONf_dihedral_angle_d6.5189589
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.997857189646 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.01-2.060.371600.36992400X-RAY DIFFRACTION90.75
2.06-2.110.35851480.3222600X-RAY DIFFRACTION98.67
2.11-2.180.31351330.3062680X-RAY DIFFRACTION99.75
2.18-2.240.34321360.28712552X-RAY DIFFRACTION99.33
2.25-2.330.30521210.28352568X-RAY DIFFRACTION99.48
2.33-2.420.321440.26872662X-RAY DIFFRACTION100
2.42-2.530.29181120.26822689X-RAY DIFFRACTION99.93
2.53-2.660.32441480.25522677X-RAY DIFFRACTION99.89
2.66-2.830.29441250.26812730X-RAY DIFFRACTION99.96
2.83-3.050.29041470.26942670X-RAY DIFFRACTION100
3.05-3.350.28161420.24262692X-RAY DIFFRACTION100
3.35-3.840.24891080.21221931X-RAY DIFFRACTION71.69
3.84-4.830.24781170.18722405X-RAY DIFFRACTION87.91
4.83-28.290.24641560.19822732X-RAY DIFFRACTION99.28
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)
14.31406494707-0.464368190706-0.04403727415173.28621802983-0.5663296483714.75475965329-0.1935247144430.721113533374-1.37725792024-0.5022762025780.180932241416-0.149048311250.796609570533-0.2956291925160.0219186465950.384475827358-0.02466061248310.1294028627840.438716047652-0.0873763502420.8215915812376.56858941381-6.275247002577.89949264084
26.98655534848-1.81065003694-0.5508582592912.59512645343-0.7711234161344.56945421010.211248512130.004241419419920.5046013486550.102639031391-0.170766043071-0.0894554503232-0.5199984848210.0166710561425-0.04134244291990.2590419788780.03374748609290.08140874882890.3604021921090.04512481882820.42905152834412.51560167546.9701578426210.4535342191
37.50823804337-0.826442486851-0.2085812511245.380002023781.431423349915.445111293980.1055363735480.5384208711230.791480559226-0.0967185756471-0.0494051470289-0.218689267458-0.5878118121570.155144435021-0.05687103495390.3004183456940.01891254094260.01524322252560.3817694243780.04395776352670.39650461422116.775796917311.97937147315.64949713803
45.64796297458-0.4732976398011.335785562212.17410765641-0.840637710444.20499801736-0.142470133672-0.353593072142-0.6828319174340.3353016043380.3313714806410.824545242364-0.0141790072707-0.653049113041-0.1636462320760.3515733170840.07445117514150.1278620085010.4136686326680.08498996360450.6359849465021.924592463161.9791101634416.1830407798
54.834209484352.29169517197-0.2836033037772.47001128528-0.6341187998554.08584673480.13958419955-0.861593177823-0.5818495378891.28055401110.1855456735620.7171251122680.410084018507-0.151985200401-0.3270123393210.7958496456010.1682446450140.2497483451250.6851972364550.2030119409270.6930513493144.95344570898-0.15389976335532.3998056731
62.02059111414-0.24731909333-4.197911269054.28938896344-0.1184439566387.458971397280.286861599533-2.222651927810.8758773503161.763194293320.3254471186080.464463808917-0.7078389190230.760641970778-0.5926748531981.137970006550.06548832799920.1221341726671.20526994371-0.1608574173640.73741406833414.04422817314.684230796636.4830544852
76.508382360391.06226098673-0.9528706818243.00167540516-0.644658247314.27508130145-0.0627849552579-0.764188127104-1.545444952880.6554904358480.1535871556360.1186845425870.437727447235-0.136678461877-0.0847754682080.4519572456670.1314525685090.1218566839070.432304437420.1722432392460.7207540807612.51624551-4.9849153263523.9681009771
89.239700074662.982586554271.820665952386.565730540130.966097911613.81755852344-0.0727378133527-0.4940739084360.9345558194770.7478654278420.0248821797124-0.0538648882583-0.1740112830830.1909305837690.05827075033260.3211225195150.0789605783801-0.008771921227160.43978231069-0.04018995407460.43547181717633.76968771345.1932910855615.1249873297
96.41534597404-1.93714846775-0.5507858400538.687757783133.94302893937.665698133130.08453179370880.202606879095-0.0627027913831-0.19557535070.0664416738319-0.9037235901830.4678474004440.127760975208-0.1464883399680.3188127154130.06303562953210.04411692084380.395829112820.02657386414830.34762017344734.2317029184-3.443909712335.00314244246
107.26321526234-2.49390311588-3.105577504157.228801881711.396111688098.234153646770.1232800988930.840364583639-0.662384377052-0.530380866819-0.3714642419450.6931612960410.334307575924-0.5937993011580.2464632319410.2964359171180.0577827471086-0.03529727613590.398563365975-0.07993903487860.47218956979127.4514873558-3.27318939274-0.431022414423
113.53740946933-0.7575953530340.4941134901414.04682629821-0.6683359234922.42216420432-0.112445049048-0.2695218499080.2344336265030.4718012172920.0924596664452-1.047897103410.1658782102930.7078488323970.0356810824530.3962893609260.129850323876-0.06022426788310.510570610411-0.1012142438410.51820498702839.7026536994-3.0889447955813.4091202135
125.21791025429-1.30590448326-0.8537753840168.822754604561.214160929596.2166046594-0.731565533033-1.550342374960.795311079442.47835634626-0.113535921816-0.695876570066-0.426422474110.8969827676420.8452504614721.274701918020.242481548873-0.3491477224291.40875091554-0.1698963410670.89247491228740.0012087621-8.7800376890330.0963518016
137.784930747292.136453898671.655196677337.252055399030.4500493667998.6567713648-0.0907903268509-1.3654872657-0.7549239717571.206669987540.1280642511310.1453663440630.735571937336-0.344214904739-0.0342236566680.4985645327280.1024476287780.06937027794350.5002229341540.1037789746930.40987923696128.8961874088-24.71194247316.7646990657
149.63591875083.12096680163-0.467347307589.04718609744-2.792820767865.523575651460.305185629585-1.775790404950.5869452226632.44817430726-0.3978714810260.04321992047470.3452779931630.1460785371840.1017036699640.8489428114190.1565888684830.01472306971540.694019542051-0.1141508417970.54371847430628.4818174461-4.0607215718725.4476947861
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 27 through 45 )AA27 - 451 - 19
22chain 'A' and (resid 46 through 76 )AA46 - 7620 - 50
33chain 'A' and (resid 77 through 102 )AA77 - 10251 - 76
44chain 'A' and (resid 103 through 176 )AA103 - 17677 - 150
55chain 'A' and (resid 177 through 258 )AA177 - 258151 - 206
66chain 'A' and (resid 259 through 299 )AA259 - 299207 - 247
77chain 'A' and (resid 300 through 345 )AA300 - 345248 - 293
88chain 'B' and (resid 30 through 58 )BB30 - 581 - 29
99chain 'B' and (resid 59 through 76 )BB59 - 7630 - 47
1010chain 'B' and (resid 77 through 90 )BB77 - 9048 - 61
1111chain 'B' and (resid 91 through 168 )BB91 - 16862 - 139
1212chain 'B' and (resid 169 through 238 )BB169 - 238140 - 159
1313chain 'B' and (resid 239 through 299 )BB239 - 299160 - 220
1414chain 'B' and (resid 300 through 343 )BB300 - 343221 - 264

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