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- PDB-8x8k: Crystal structure of STBD1 CBM20 domain in complex with maltotetraose -

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Basic information

Entry
Database: PDB / ID: 8x8k
TitleCrystal structure of STBD1 CBM20 domain in complex with maltotetraose
ComponentsStarch-binding domain-containing protein 1
KeywordsPROTEIN BINDING / STBD1 / CBM20 / maltotetraose
Function / homology
Function and homology information


substrate localization to autophagosome / glycogen binding / glycophagy / starch binding / phagophore assembly site membrane / RHOD GTPase cycle / glycogen catabolic process / cargo receptor activity / polysaccharide binding / tertiary granule membrane ...substrate localization to autophagosome / glycogen binding / glycophagy / starch binding / phagophore assembly site membrane / RHOD GTPase cycle / glycogen catabolic process / cargo receptor activity / polysaccharide binding / tertiary granule membrane / ficolin-1-rich granule membrane / RHOG GTPase cycle / RHOA GTPase cycle / RAC2 GTPase cycle / RAC3 GTPase cycle / intracellular transport / T-tubule / Neutrophil degranulation / endoplasmic reticulum membrane / perinuclear region of cytoplasm / enzyme binding / endoplasmic reticulum / membrane / plasma membrane
Similarity search - Function
Starch-binding domain-containing protein 1, CBM20 domain / Carbohydrate binding module family 20 / Starch binding domain / CBM20 (carbohydrate binding type-20) domain profile. / Starch binding domain / Carbohydrate-binding-like fold / Immunoglobulin-like fold
Similarity search - Domain/homology
alpha-maltotetraose / Starch-binding domain-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsZhang, Y.C. / Pan, L.F.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2024
Title: Decoding the molecular mechanism of selective autophagy of glycogen mediated by autophagy receptor STBD1.
Authors: Zhang, Y. / Sun, Y. / Shi, J. / Xu, P. / Wang, Y. / Liu, J. / Gong, X. / Wang, Y. / Tang, Y. / Liu, H. / Zhou, X. / Lin, Z. / Baba, O. / Morita, T. / Yu, B. / Pan, L.
History
DepositionNov 27, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 18, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Starch-binding domain-containing protein 1
B: Starch-binding domain-containing protein 1
C: Starch-binding domain-containing protein 1
D: Starch-binding domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,46313
Polymers46,1874
Non-polymers4,2769
Water2,036113
1
A: Starch-binding domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,8803
Polymers11,5471
Non-polymers1,3332
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Starch-binding domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,2132
Polymers11,5471
Non-polymers6671
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Starch-binding domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,9724
Polymers11,5471
Non-polymers1,4253
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Starch-binding domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,3984
Polymers11,5471
Non-polymers8513
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.879, 74.879, 163.087
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

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Components

#1: Protein
Starch-binding domain-containing protein 1


Mass: 11546.822 Da / Num. of mol.: 4 / Fragment: CBM20 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: STBD1 / Production host: Escherichia coli (E. coli) / References: UniProt: O95210
#2: Polysaccharide
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Substrate analog / Mass: 666.578 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltotetraose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,4,3/[a2122h-1a_1-5]/1-1-1-1/a4-b1_b4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}}}LINUCSPDB-CARE
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 113 / 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: 2.86 Å3/Da / Density % sol: 56.96 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.09 M Halogens (0.3M Sodium fluoride; 0.3M Sodium bromide; 0.3M Sodium iodide), 0.1 M Buffer System 1 (Imidazole; MES (acid) pH 6.5), 37.5% v/v Precipitant Mix 4 (25% v/v MPD (racemic); 25% ...Details: 0.09 M Halogens (0.3M Sodium fluoride; 0.3M Sodium bromide; 0.3M Sodium iodide), 0.1 M Buffer System 1 (Imidazole; MES (acid) pH 6.5), 37.5% v/v Precipitant Mix 4 (25% v/v MPD (racemic); 25% PEG 1000; 25% w/v PEG 3350)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.97903 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 19, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97903 Å / Relative weight: 1
ReflectionResolution: 2.1→64.574 Å / Num. obs: 67178 / % possible obs: 100 % / Redundancy: 13.7 % / Biso Wilson estimate: 48.2 Å2 / Rmerge(I) obs: 0.113 / Net I/σ(I): 12.7
Reflection shellResolution: 2.168→2.206 Å / Rmerge(I) obs: 0.78 / Num. unique obs: 1398

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Processing

Software
NameVersionClassification
PHENIX1.19rc4_4035refinement
AutoProcessdata reduction
AutoProcessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold

Resolution: 2.1→41.66 Å / SU ML: 0.2683 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 26.167
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2263 1581 4.96 %
Rwork0.1865 30294 -
obs0.1885 31875 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 57.33 Å2
Refinement stepCycle: LAST / Resolution: 2.1→41.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3188 0 288 113 3589
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00863607
X-RAY DIFFRACTIONf_angle_d1.14564966
X-RAY DIFFRACTIONf_chiral_restr0.0706597
X-RAY DIFFRACTIONf_plane_restr0.0084568
X-RAY DIFFRACTIONf_dihedral_angle_d7.945422
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.160.29341590.25872700X-RAY DIFFRACTION99.97
2.16-2.240.3041390.24952703X-RAY DIFFRACTION99.89
2.24-2.330.26441620.23452707X-RAY DIFFRACTION100
2.33-2.440.28531090.23992725X-RAY DIFFRACTION99.96
2.44-2.570.29191340.24672736X-RAY DIFFRACTION99.97
2.57-2.730.32391410.25692722X-RAY DIFFRACTION100
2.73-2.940.26231350.22882747X-RAY DIFFRACTION100
2.94-3.230.29341440.22852758X-RAY DIFFRACTION100
3.23-3.70.24381580.17792754X-RAY DIFFRACTION99.97
3.7-4.660.18241630.15372794X-RAY DIFFRACTION99.97
4.66-41.660.17821370.15142948X-RAY DIFFRACTION99.9
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)
13.845147809282.870890393943.154502239278.563633557885.458636231248.451596521140.34462786345-0.110307038053-0.2518318433240.823249833178-0.151066481467-0.2415577503461.005906114160.128470392401-0.4286357420560.6112571887050.035895141877-0.07145427712130.4766168227190.1207292373640.426279854921-20.9899716652-27.572480860224.7676954014
24.562345392621.464378541630.4365966879278.645172193741.607024790266.524329242370.284878823040.351448041229-0.617107046867-0.08014808277350.310622629826-1.140926501650.2966858356420.561753499051-0.4966209507180.3157513622030.0967668346204-0.1037462019780.4442998763170.03262815749180.457918811768-17.1580578323-30.020502583812.5604611644
38.674883283372.061082534030.4141388301632.414121629641.034099330957.401165846810.3182563520650.307475078163-0.977423262395-0.142186990244-0.0353372687874-0.9096654503770.281073938954-0.0408338832163-0.2787253783730.3702663591770.108194650441-0.05662613961860.444097857423-0.00941122702480.458271382351-14.6319720813-28.205702261115.2840549952
43.16844787897-0.546762647479-0.3299705520865.658841907432.154908869747.215429014150.101759417005-0.0956086321496-0.271780522610.05261986831110.03853602726830.112137613880.424957859210.163301527475-0.08916418365510.2717347125240.0669458724812-0.05459747502890.3170568584640.06213978103180.375854763771-21.2164573043-24.814729025417.7415919403
54.779515457873.04436020152-1.313088583655.803152348320.08313055973576.48339462340.5319995950010.5469814960931.34223262480.191117604240.4246658773290.9729333483450.0520514964253-0.8912666908370.09658053718230.503403079430.0724641070431-0.1891998849770.441326715190.008937950099570.531621458421-30.2301905202-25.299660741412.5488861879
69.24228977842-2.083767228852.103720363426.11990400291-1.322269262234.046635137860.4567895025990.634352346204-0.814282126412-0.421399965247-0.01072363921040.06532968564950.4103989527220.0957196813379-0.417172694880.388588557680.00681606326965-0.006048168327780.271825166128-0.04882118929460.294650373573-22.5495617059-3.796261720915.7690461019
76.652885954823.926092155444.207720336342.734918494452.908220228744.628154185750.0259537660251-0.0101692415173-1.21465486914-0.3415417001950.199126409501-1.25966383150.1431129466531.13499024606-0.1429046518330.545968034224-0.0187355532960.1378474863640.5959408478350.06225776810680.604522842029-14.66356311070.82847858575410.2774530675
86.050563973570.378985610424-0.4527404244891.697614481040.5348843159630.7498062561850.1049098205920.2275220355880.179281988682-0.8045290873250.0560294114803-0.07829175294440.13925158040.418325382246-0.2982728104510.5508501478270.08046154442940.0807235754060.42255836533-0.01977827135230.390996428925-20.8829893295-3.0307027768311.5344148733
93.60239451404-0.3122309074880.3399038644515.76543686459-0.5709351827445.25384384713-0.0933651959948-0.008568257793580.20109448764-0.1744223215030.0900001599922-0.530482869117-0.2923190509350.564882524849-0.009042830353020.335587962248-0.008440224658520.05629097549350.3734891511690.001919273349340.31793940419-17.11485627392.0635920554116.8407194725
106.62136304683.446185454735.626565559558.164571889744.217277582799.398557126130.123905949645-0.7156004433590.04179718983790.0960533365275-0.0905482863734-0.320723392077-0.09151226234390.00962042210384-0.04983052954670.3501976573340.0428173195209-0.04084781887020.5138641248620.01442885412850.394905580925-36.5336156238-22.3729696893-2.82693062918
116.84448776869-0.1251460734241.462366153751.478704976460.3141302957035.550120104150.5076551166260.701119227808-1.729344825720.0009212004231960.0893412548784-0.955121312140.8083428539960.290879165865-0.4858250473620.2985576001290.0584877471398-0.1054712016120.44478219095-0.09183302751520.538570430335-36.3405712892-30.6542255711-14.0123742285
126.90617238320.7260300239520.9840333604215.371743839420.03959074783646.021099652920.09481076791890.246112395208-0.429658646167-0.2926915072830.0587125343757-0.2457879294380.1293247462370.420027233012-0.07447485831370.285733961590.0199892792161-0.07078394073350.389577473079-0.001094358274550.381383701725-36.0049923154-26.1607761446-12.3353379595
136.41600597952-0.472083448108-2.08384704424.287830495793.218759859454.216598632270.137968336252-0.9950102692321.022406223210.4922824147550.2883851942670.0076698795206-1.23529645631-0.51245315957-0.2559368308070.748822072777-0.0438256491621-0.08004187778890.601925146928-0.02466089579470.520972635261-37.220368652-14.2093506939-4.21592916977
148.98536322958-1.214000420611.456912914369.158519261713.783046927898.76766612657-0.446451434788-1.0525135171-0.5210338093860.592487826272-0.03699258518511.393134279230.673144622202-0.8887477645740.07930189917390.3978670264380.0437208814355-0.08511534198290.4470337426750.0420973523780.510013803248-43.5622605408-21.1096155928-4.54424571396
155.182156513811.67006330245-0.9056146195422.77904857115-2.415035871637.50757904202-0.4421265009870.6604393783061.175650433210.6373820455460.843972664440.216146366629-0.276442973112-0.733336005835-0.2432206057220.374454524290.00488151385665-0.1895582959050.5010099478550.003368983209260.560390626095-46.6577663169-21.802476197-16.0412945062
168.394965242170.382058578009-1.570329588763.527600156631.639624791111.581488634040.0231395623658-1.00598024222-1.57248340050.2079947985590.7354920884050.6029530053690.472005209762-0.762160798408-0.543080988380.467776244295-0.108873582815-0.1402140333030.7461963316530.313806619210.520236970547-48.4170192282-33.3318299712.4119132972
175.60672389346-0.7342106031740.8510927811276.961235958762.910844576915.471184283860.473449799346-1.51742535375-1.113974842420.3477529615050.07239621158190.254932964333-0.0350502958054-0.851608643857-0.4022348519920.734424122432-0.019974638593-0.03914850380811.151139301550.3354763723550.82900513318-51.7271778413-31.375454621617.0122458509
186.82389205122-0.5060375698522.547323884624.97890798157-0.3503345537775.435681084380.0370348430201-2.96572428228-0.6801575489980.5902152358550.5216572815470.8009732894410.148250264793-1.53461184436-0.4726024587370.507675744989-0.0902555038462-0.09079305673690.9738352308830.3277010499620.532791459652-53.2325589783-28.039552529513.8052488335
196.874806429660.5329748758480.9902737926244.778546035012.136538458595.622998246660.011760908037-0.7641001612770.265756767989-0.1308561708130.1633393482740.0322796766915-0.345001239682-0.520101458548-0.3965500857040.424494349346-0.02053879922090.01467534493670.5903578231960.1539383384560.387697027035-50.4208555954-24.538027327212.4059573895
207.309809993030.230373009624-0.04685489831118.036617522216.954684646796.912629962360.1537817549530.4289775602010.643700961342-1.35734082695-0.652848684230.93277916358-1.85267497344-0.3962111544940.5061511012920.4775532349160.000373846546966-0.06377093042230.6497783165230.1746436351670.589724247344-43.1478393661-23.93249289546.95977808163
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 262 through 271 )AA262 - 2711 - 10
22chain 'A' and (resid 272 through 290 )AA272 - 29011 - 29
33chain 'A' and (resid 291 through 302 )AA291 - 30230 - 41
44chain 'A' and (resid 303 through 353 )AA303 - 35342 - 92
55chain 'A' and (resid 354 through 358 )AA354 - 35893 - 97
66chain 'B' and (resid 262 through 279 )BC262 - 2791 - 18
77chain 'B' and (resid 280 through 290 )BC280 - 29019 - 29
88chain 'B' and (resid 291 through 305 )BC291 - 30530 - 44
99chain 'B' and (resid 306 through 358 )BC306 - 35845 - 97
1010chain 'C' and (resid 261 through 271 )CE261 - 2711 - 11
1111chain 'C' and (resid 272 through 290 )CE272 - 29012 - 30
1212chain 'C' and (resid 291 through 339 )CE291 - 33931 - 79
1313chain 'C' and (resid 340 through 348 )CE340 - 34880 - 88
1414chain 'C' and (resid 349 through 353 )CE349 - 35389 - 93
1515chain 'C' and (resid 354 through 358 )CE354 - 35894 - 98
1616chain 'D' and (resid 262 through 285 )DH262 - 2851 - 24
1717chain 'D' and (resid 286 through 305 )DH286 - 30525 - 44
1818chain 'D' and (resid 306 through 327 )DH306 - 32745 - 66
1919chain 'D' and (resid 328 through 353 )DH328 - 35367 - 92
2020chain 'D' and (resid 354 through 358 )DH354 - 35893 - 97

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