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- PDB-7kma: Crystal structure of eif2Balpha with a ligand. -

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Basic information

Entry
Database: PDB / ID: 7kma
TitleCrystal structure of eif2Balpha with a ligand.
ComponentsTranslation initiation factor eIF-2B subunit alpha
KeywordsSUGAR BINDING PROTEIN / Translation initiation factor eif-2b / translation factor activity / RNA binding / translation regulator activity / nucleic acid binding
Function / homology
Function and homology information


eukaryotic translation initiation factor 2B complex / Recycling of eIF2:GDP / cytoplasmic translational initiation / oligodendrocyte development / response to glucose / translational initiation / translation initiation factor activity / guanyl-nucleotide exchange factor activity / response to peptide hormone / response to heat ...eukaryotic translation initiation factor 2B complex / Recycling of eIF2:GDP / cytoplasmic translational initiation / oligodendrocyte development / response to glucose / translational initiation / translation initiation factor activity / guanyl-nucleotide exchange factor activity / response to peptide hormone / response to heat / T cell receptor signaling pathway / membrane / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Translation initiation factor eIF-2B subunit alpha, N-terminal / Initiation factor 2B-related / Initiation factor 2B-like, C-terminal / Initiation factor 2 subunit family / NagB/RpiA transferase-like
Similarity search - Domain/homology
ACETATE ION / 6-O-phosphono-alpha-D-mannopyranose / Translation initiation factor eIF2B subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsNocek, B. / Hao, Q. / Remarcik, C. / Stoll, V. / Wong, Y. / Sidrauski, C.
CitationJournal: Nat Commun / Year: 2021
Title: Sugar phosphate activation of the stress sensor eIF2B.
Authors: Qi Hao / Jin-Mi Heo / Boguslaw P Nocek / Kevin G Hicks / Vincent S Stoll / Clint Remarcik / Sean Hackett / Lauren LeBon / Rinku Jain / Dan Eaton / Jared Rutter / Yao Liang Wong / Carmela Sidrauski /
Abstract: The multi-subunit translation initiation factor eIF2B is a control node for protein synthesis. eIF2B activity is canonically modulated through stress-responsive phosphorylation of its substrate eIF2. ...The multi-subunit translation initiation factor eIF2B is a control node for protein synthesis. eIF2B activity is canonically modulated through stress-responsive phosphorylation of its substrate eIF2. The eIF2B regulatory subcomplex is evolutionarily related to sugar-metabolizing enzymes, but the biological relevance of this relationship was unknown. To identify natural ligands that might regulate eIF2B, we conduct unbiased binding- and activity-based screens followed by structural studies. We find that sugar phosphates occupy the ancestral catalytic site in the eIF2Bα subunit, promote eIF2B holoenzyme formation and enhance enzymatic activity towards eIF2. A mutant in the eIF2Bα ligand pocket that causes Vanishing White Matter disease fails to engage and is not stimulated by sugar phosphates. These data underscore the importance of allosteric metabolite modulation for proper eIF2B function. We propose that eIF2B evolved to couple nutrient status via sugar phosphate sensing with the rate of protein synthesis, one of the most energetically costly cellular processes.
History
DepositionNov 2, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 21, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Translation initiation factor eIF-2B subunit alpha
B: Translation initiation factor eIF-2B subunit alpha
C: Translation initiation factor eIF-2B subunit alpha
D: Translation initiation factor eIF-2B subunit alpha
E: Translation initiation factor eIF-2B subunit alpha
F: Translation initiation factor eIF-2B subunit alpha
G: Translation initiation factor eIF-2B subunit alpha
H: Translation initiation factor eIF-2B subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)279,44517
Polymers277,3058
Non-polymers2,1409
Water2,756153
1
A: Translation initiation factor eIF-2B subunit alpha
C: Translation initiation factor eIF-2B subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,9065
Polymers69,3262
Non-polymers5793
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4120 Å2
ΔGint-25 kcal/mol
Surface area22950 Å2
MethodPISA
2
B: Translation initiation factor eIF-2B subunit alpha
H: Translation initiation factor eIF-2B subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,8464
Polymers69,3262
Non-polymers5202
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3770 Å2
ΔGint-26 kcal/mol
Surface area23170 Å2
MethodPISA
3
D: Translation initiation factor eIF-2B subunit alpha
E: Translation initiation factor eIF-2B subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,8464
Polymers69,3262
Non-polymers5202
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4030 Å2
ΔGint-25 kcal/mol
Surface area22980 Å2
MethodPISA
4
F: Translation initiation factor eIF-2B subunit alpha
G: Translation initiation factor eIF-2B subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,8464
Polymers69,3262
Non-polymers5202
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4100 Å2
ΔGint-24 kcal/mol
Surface area23090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.200, 155.540, 140.110
Angle α, β, γ (deg.)90.000, 103.893, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
Translation initiation factor eIF-2B subunit alpha / eIF-2B GDP-GTP exchange factor subunit alpha


Mass: 34663.098 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EIF2B1, EIF2BA / Production host: Escherichia coli (E. coli) / References: UniProt: Q14232
#2: Sugar
ChemComp-M6P / 6-O-phosphono-alpha-D-mannopyranose / ALPHA-D-MANNOSE-6-PHOSPHATE / 6-O-phosphono-alpha-D-mannose / 6-O-phosphono-D-mannose / 6-O-phosphono-mannose


Type: D-saccharide, alpha linking / Mass: 260.136 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C6H13O9P / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
a-D-Manp6PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 153 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.98 Å3/Da / Density % sol: 58.67 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 12% PEG 4000, 100 mM sodium acetate, 100 mM ammonium sulfate, 0.5% octyl-beta-glucoside, pH 4.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→55.61 Å / Num. obs: 150142 / % possible obs: 93.7 % / Redundancy: 1.9 % / Biso Wilson estimate: 59.66 Å2 / Rpim(I) all: 0.036 / Net I/σ(I): 2
Reflection shellResolution: 2.7→2.797 Å / Num. unique obs: 15063 / Rpim(I) all: 0.32 / % possible all: 99.64

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Processing

Software
NameVersionClassification
PHENIXdev_3916refinement
XDSdata reduction
pointlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ECS
Resolution: 2.7→55.61 Å / SU ML: 0.3434 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 24.4496
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2382 3881 5.09 %
Rwork0.1909 72313 -
obs0.1933 76194 93.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 68.15 Å2
Refinement stepCycle: LAST / Resolution: 2.7→55.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16840 0 132 153 17125
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008217290
X-RAY DIFFRACTIONf_angle_d0.925523505
X-RAY DIFFRACTIONf_chiral_restr0.05742896
X-RAY DIFFRACTIONf_plane_restr0.00432936
X-RAY DIFFRACTIONf_dihedral_angle_d20.60916013
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.730.38851200.31222719X-RAY DIFFRACTION96.7
2.73-2.770.30431580.27072706X-RAY DIFFRACTION99.79
2.77-2.80.28891360.24342751X-RAY DIFFRACTION99.55
2.8-2.840.29631460.24032740X-RAY DIFFRACTION99.86
2.84-2.880.31661340.23662756X-RAY DIFFRACTION99.72
2.88-2.920.29881730.22942722X-RAY DIFFRACTION99.76
2.92-2.970.28521730.23532727X-RAY DIFFRACTION99.69
2.97-3.020.3061370.24182717X-RAY DIFFRACTION99.93
3.02-3.070.28231410.24482772X-RAY DIFFRACTION99.93
3.07-3.130.3171480.25322769X-RAY DIFFRACTION100
3.13-3.190.33981240.22532757X-RAY DIFFRACTION99.93
3.19-3.250.26031310.21772779X-RAY DIFFRACTION99.66
3.25-3.320.27471640.20832694X-RAY DIFFRACTION99.72
3.32-3.40.27021200.20942784X-RAY DIFFRACTION99.86
3.4-3.410.2172130.2204240X-RAY DIFFRACTION73.55
3.49-3.580.26991500.2082516X-RAY DIFFRACTION97.05
3.58-3.680.26371160.20482050X-RAY DIFFRACTION75.05
3.68-3.80.261410.19382744X-RAY DIFFRACTION99.35
3.8-3.940.2122810.18121690X-RAY DIFFRACTION60.73
3.94-4.10.23421250.17732736X-RAY DIFFRACTION99.03
4.1-4.280.2091690.16272733X-RAY DIFFRACTION99.35
4.28-4.510.20361800.15152693X-RAY DIFFRACTION99.07
4.51-4.790.18821550.14742732X-RAY DIFFRACTION99.24
4.79-5.160.20351300.16182771X-RAY DIFFRACTION99.52
5.16-5.680.22371730.18212731X-RAY DIFFRACTION99.62
5.68-6.50.24821610.20022746X-RAY DIFFRACTION99.25
6.5-8.180.22431460.17362743X-RAY DIFFRACTION98.8
8.19-55.610.1821360.16952795X-RAY DIFFRACTION98.22
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)
13.21396300707-0.6085213009921.880007504843.08544421010.9365783336167.910664688650.07572674382830.637458805347-0.105627006617-0.461163133657-0.140350625097-0.2416773040980.9520745557830.249127512388-0.07111465659290.679997016030.005016617969020.2018558235740.6716194946370.01726329429090.60460167289142.214594800952.859846522881.2923785229
23.917531665121.627363380912.565391153442.556117131350.1444148405566.99463252029-0.3616726767350.6158012299770.0347013774602-0.6130837576910.135602851628-0.347344285466-0.3976195419710.3449203534310.2200715227290.3947868014090.07027748221820.07834427274170.5794533629130.1100552883360.51057148300944.661740951468.012450149492.8175694227
32.393760139910.6667639344081.213292442191.80274733075-0.2039907879923.24356956331-0.1284442917870.0117407712494-0.108370553501-0.00203787590268-0.0325811332492-0.1302770543590.1275859486860.1656138016180.1295230030770.2280249640960.07071535840440.09284655607090.4445563093380.1177114052090.38608921746738.888425223260.9230566417105.687535595
40.939398799950.04369225486810.6398622277413.94012596918-1.243267034261.5960481345-0.3360726478020.658253527842-0.560129974060.3036348136880.9033433666891.539975008030.0563505604552-0.665769558025-0.5414361625290.48868999105-0.01954338029720.2010456630560.80305982352-0.02844948755991.20213615003-7.6064873389348.5734009358101.428007623
54.841406444640.09364927634053.348287809312.12235138566-2.994632604638.31892599277-0.3646205429490.248901999787-1.527179138520.1732194321150.715671950324-0.7161764376650.9345851522830.379759150779-0.4225652951120.7713883791480.1048648096280.1752828701270.877405735935-0.09875453689361.1254188221.539587097844.8276504641104.926569776
61.705390465941.30069895608-0.06524588917957.33206276708-1.569605278150.364966872897-0.05847018960560.553400019672-1.047252143610.0901233823973-0.27180731387-0.8147052226180.450809471530.2452920604650.2451903071450.460280513152-0.1081609890210.04842483818340.759016753145-0.363814543061.231491733428.9713404522150.0135388299108.054242104
76.245625256450.1712800284882.249433765572.90274046369-0.9487475836324.17375903366-0.616040137733-0.319979209381-0.07414317445671.159402116760.4224871460560.282757676331-0.181858256736-0.5908401674020.03825260605010.6187554788490.05485067731890.1049425305240.8883131114920.06981698297560.4294910193941.8135163390964.0219523795109.287092711
82.30107635416-1.024006566680.7923223145513.00474194658-0.723738741953.14547111115-0.0622802255791-0.285388431125-0.201619564574-0.08844497952410.1308297924440.1046397685390.0310635288125-0.216168119214-0.05692514004690.202569804804-0.05579776078140.02399656836060.3522411623410.06399987927960.2876329105884.2084660409668.188249449191.2793206834
94.95988540221-0.4240269880541.993912799794.12726785757-1.532871356075.664223873270.360539474826-0.2718357997210.1658119401930.543518223426-0.398799877842-0.8618712292350.5196038943560.2908730107850.00578211833130.603699167587-0.0132866202753-0.09345660709780.6061335959820.200626805550.74860579866648.731273810644.4028764756150.363532945
101.73810621310.8648305343420.532167119843.072450263760.6338737984714.921592679310.104872407928-0.0938133297773-0.1064815775690.215788194776-0.0564445092665-0.1270627853720.4262797532960.0852325577758-0.04361281433780.3217374494870.04395005339570.04341610467260.3704653948430.1452851569820.40128891171636.663287877448.9186707369129.408639307
115.55244256212-2.62460945138-0.314318754464.32081680282-0.4045299628155.64384754004-0.455470888648-0.3306638677881.537820781630.202020880630.183370575996-0.37354700371-0.699850783247-0.5099597914460.1944305546010.4748511690260.00106552034233-0.1890473564690.687924607468-0.06822013085211.066610447561.52543580647109.943004837115.698031666
123.28901729777-1.338783316011.707657741483.10584370817-2.516887249545.804693942550.0322987042717-0.1883137484740.116607299082-0.2500130509290.1520573208410.4762053300830.38196955252-0.732890679323-0.2496492803350.364404330882-0.0979987657369-0.02858092995050.5879574640060.03409305814020.5118766000011.320963020588.1405981595119.679223913
133.084078297960.2955859503910.3927704145023.23935371626-1.766604165395.06662293347-0.131447049709-0.08085787538110.265792776654-0.06659306882570.09078693104010.01563013171110.042247520471-0.1472339551520.0541699494890.225463215074-0.00880398933360.006562208100790.327840892553-0.01817824831350.33857255984715.325423932689.9379901476122.272635812
142.78119438476-0.141929814480.8194457592152.60710388074-1.891534559235.12223681249-0.263854728551-0.429051340227-0.02415773927330.7332129069180.100691002327-0.000222606332171-0.0111672766331-1.066869619890.1709750345330.942029172569-0.0279548117862-0.01148359671291.11992399015-0.08329786267290.48963722871927.178044614370.9892209778166.515499682
152.61897811411-0.6410351176020.7173427095094.55082737846-0.7278004158552.68547013157-0.158803948156-0.4191385928770.1170391452850.5684894295670.135339421625-0.129536999184-0.0213346428753-0.2114450584120.02529871355050.4074248395750.0235234283245-0.03795618626560.483092715483-0.05188886155780.27795474631328.658358164382.8664133174145.294874516
163.974874871290.4987412376291.264477094075.06056752670.4644751867995.54486199807-0.203884430961-0.4928426890170.8722995276040.3310610761230.489739634176-0.435199932694-0.04069408065550.301392175068-0.283547386030.3700961271910.00881574927259-0.02511836856420.65491813758-0.2072082017360.73838056437548.3177462987102.497395756114.039614128
171.06637461911-0.457599915011-0.1592269350570.5540799704290.1197958504265.529976248590.156916316525-0.04217721933270.034178966056-0.1498550091370.0460762455790.0204664855660.1554376028850.169486595721-0.1887459742330.383881553656-0.0787289978282-0.008801341366060.2758258757590.02522257737750.45148413561935.30263023297.595134695893.8635928
185.78603809971-0.8461245344180.4663660074033.50549329704-1.706539107165.85747215675-0.2396511299740.3538950384350.396441366450.0607199717245-0.283319701106-0.467484303729-0.6933189417430.6863295375180.5042308134940.881083218095-0.07134099812270.08413117573550.574666629910.08881649658360.78384487790324.9257063882115.6490515549.718703719
190.610466001231-0.0878330116214-0.2355237664141.211078978340.8737420427816.518429695060.04738758888650.2660491449920.0351042074008-0.598698673215-0.1275679405030.177998110393-0.608721743735-0.7895785174790.05530037245530.8916878754140.0116241291628-0.07599447218470.5165114835820.07680430723470.61867516292712.3104776142115.28000011859.7597421131
201.909956111840.2222451215780.396629483472.34141998250.4539317180663.301226425510.1789243545770.0485408660936-0.0193094208266-0.192535389851-0.0721307959316-0.0888933329106-0.267516542926-0.0965780723847-0.0860601137220.429463290138-0.0193320048350.03801799984120.2357745062790.07017800982970.39124487293419.5165890781108.29805422375.0395984955
215.54043667966-0.6653067285120.9944852287642.67594740396-0.1392812865133.974053635090.1150392556860.3961518918320.186376456334-0.497306062753-0.1304682007910.598432386119-0.257806154609-0.6034259835070.0487063047020.9188001237240.00599994230387-0.09810298295070.723095077244-0.0312267089520.471493855018-6.0999569581486.489496247746.6249993792
222.30568601835-0.416130955825-0.3113200617553.52701933198-0.4883950618352.9956470631-0.01744003691740.183440619382-0.0886184272054-0.432458951920.0270395448768-0.0362931252239-0.107825508948-0.0637889678671-0.01772408739310.394324419668-0.0689577177639-0.02639942114450.280464944971-0.01214839108540.2921929480758.2028759102474.43283171764.0548519534
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 2 through 85 )AA2 - 851 - 77
22chain 'A' and (resid 86 through 143 )AA86 - 14378 - 135
33chain 'A' and (resid 144 through 306 )AA144 - 306136 - 287
44chain 'B' and (resid 4 through 21 )BD4 - 211 - 18
55chain 'B' and (resid 22 through 62 )BD22 - 6219 - 49
66chain 'B' and (resid 63 through 92 )BD63 - 9250 - 66
77chain 'B' and (resid 93 through 118 )BD93 - 11867 - 92
88chain 'B' and (resid 119 through 306 )BD119 - 30693 - 268
99chain 'C' and (resid 1 through 118 )CF1 - 1181 - 118
1010chain 'C' and (resid 119 through 306 )CF119 - 306119 - 294
1111chain 'D' and (resid 1 through 86 )DH1 - 861 - 76
1212chain 'D' and (resid 87 through 170 )DH87 - 17077 - 160
1313chain 'D' and (resid 171 through 306 )DH171 - 306161 - 284
1414chain 'E' and (resid 3 through 114 )EJ3 - 1141 - 101
1515chain 'E' and (resid 115 through 305 )EJ115 - 305102 - 278
1616chain 'F' and (resid 1 through 118 )FL1 - 1181 - 112
1717chain 'F' and (resid 119 through 306 )FL119 - 306113 - 287
1818chain 'G' and (resid 1 through 62 )GN1 - 621 - 60
1919chain 'G' and (resid 63 through 143 )GN63 - 14361 - 141
2020chain 'G' and (resid 144 through 306 )GN144 - 306142 - 290
2121chain 'H' and (resid 1 through 114 )HP1 - 1141 - 112
2222chain 'H' and (resid 115 through 306 )HP115 - 306113 - 289

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