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- PDB-5ldd: Crystal structure of the heterodimeric GEF Mon1-Ccz1 in complex w... -

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Basic information

Entry
Database: PDB / ID: 5ldd
TitleCrystal structure of the heterodimeric GEF Mon1-Ccz1 in complex with Ypt7
Components
  • Ccz1
  • Mon1
  • Rab small monomeric GTPase-like protein
KeywordsPROTEIN TRANSPORT / heterodimeric GEF protein / endosomal maturation / Rab GTPase
Function / homology
Function and homology information


Mon1-Ccz1 complex / regulation of vacuole fusion, non-autophagic / protein targeting to vacuole / multivesicular body membrane / fungal-type vacuole membrane / vesicle-mediated transport / autophagy / late endosome / GTPase activity / GTP binding
Similarity search - Function
Vacuolar fusion protein Ccz1 / Vacuolar fusion protein Mon1 / CCZ1/INTU/HSP4, first Longin domain / First Longin domain of INTU, CCZ1 and HPS4 / FUZ/MON1/HPS1, third Longin domain / FUZ/MON1/HPS1, second Longin domain / FUZ/MON1/HPS1, first Longin domain / First Longin domain of FUZ, MON1 and HPS1 / Second Longin domain of FUZ, MON1 and HPS1 / Third Longin domain of FUZ, MON1 and HPS1 ...Vacuolar fusion protein Ccz1 / Vacuolar fusion protein Mon1 / CCZ1/INTU/HSP4, first Longin domain / First Longin domain of INTU, CCZ1 and HPS4 / FUZ/MON1/HPS1, third Longin domain / FUZ/MON1/HPS1, second Longin domain / FUZ/MON1/HPS1, first Longin domain / First Longin domain of FUZ, MON1 and HPS1 / Second Longin domain of FUZ, MON1 and HPS1 / Third Longin domain of FUZ, MON1 and HPS1 / Small GTPase Rab domain profile. / Small GTPase Rho domain profile. / Small GTPase Ras domain profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CCZ1/INTU/HSP4 first Longin domain-containing protein / Rab small monomeric GTPase-like protein / Vacuolar fusion protein MON1
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.496 Å
AuthorsKiontke, S. / Kuemmel, D.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research FoundationKU2531/2-1 Germany
German Research FoundationSFB944P17 Germany
CitationJournal: Nat Commun / Year: 2017
Title: Architecture and mechanism of the late endosomal Rab7-like Ypt7 guanine nucleotide exchange factor complex Mon1-Ccz1.
Authors: Kiontke, S. / Langemeyer, L. / Kuhlee, A. / Schuback, S. / Raunser, S. / Ungermann, C. / Kummel, D.
History
DepositionJun 24, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 18, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 14, 2018Group: Author supporting evidence / Data collection / Category: diffrn_source / pdbx_audit_support
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_audit_support.funding_organization
Revision 1.2Apr 9, 2025Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 1, 2025Group: Advisory / Derived calculations / Category: pdbx_validate_close_contact / struct_conn

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Mon1
B: Ccz1
C: Rab small monomeric GTPase-like protein
D: Mon1
E: Ccz1
F: Rab small monomeric GTPase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,5579
Polymers138,2696
Non-polymers2883
Water2,198122
1
A: Mon1
B: Ccz1
C: Rab small monomeric GTPase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,3265
Polymers69,1343
Non-polymers1922
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5130 Å2
ΔGint-67 kcal/mol
Surface area24710 Å2
MethodPISA
2
D: Mon1
E: Ccz1
F: Rab small monomeric GTPase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,2304
Polymers69,1343
Non-polymers961
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4910 Å2
ΔGint-53 kcal/mol
Surface area23540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.083, 103.812, 206.667
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Mon1


Mass: 18259.047 Da / Num. of mol.: 2 / Fragment: UNP residues 195-355
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Gene: CTHT_0067370 / Production host: Escherichia coli (E. coli) / References: UniProt: G0SGS3
#2: Protein Ccz1


Mass: 27657.125 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Gene: CTHT_0050970 / Production host: Escherichia coli (E. coli) / References: UniProt: G0SD94
#3: Protein Rab small monomeric GTPase-like protein


Mass: 23218.189 Da / Num. of mol.: 2 / Mutation: N125I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Gene: CTHT_0065990 / Production host: Escherichia coli (E. coli) / References: UniProt: G0SGE1
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / 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: 2.72 Å3/Da / Density % sol: 54.7 %
Crystal growTemperature: 285.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.15 M ammonium sulfate, 0.1 M MES, pH 6.0, and 18% PEG 4000, 25% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.97951 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 30, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97951 Å / Relative weight: 1
ReflectionResolution: 2.49→46.38 Å / Num. obs: 53101 / % possible obs: 99.5 % / Redundancy: 6.53 % / Biso Wilson estimate: 69.32 Å2 / Rrim(I) all: 0.076 / Net I/σ(I): 15.24
Reflection shellResolution: 2.49→2.65 Å / Mean I/σ(I) obs: 2.62 / Rrim(I) all: 0.909 / % possible all: 98.1

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Processing

Software
NameVersionClassification
PHENIXdev_2439refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.496→46.38 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 26.73
RfactorNum. reflection% reflection
Rfree0.2411 1839 3.98 %
Rwork0.2 --
obs0.2016 46240 86.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.496→46.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7533 0 15 122 7670
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0047690
X-RAY DIFFRACTIONf_angle_d0.6210403
X-RAY DIFFRACTIONf_dihedral_angle_d15.6214594
X-RAY DIFFRACTIONf_chiral_restr0.0451198
X-RAY DIFFRACTIONf_plane_restr0.0041306
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4957-2.56310.3686480.25171061X-RAY DIFFRACTION28
2.5631-2.63860.3352790.24471965X-RAY DIFFRACTION51
2.6386-2.72370.2871150.23682644X-RAY DIFFRACTION68
2.7237-2.8210.26231360.24473228X-RAY DIFFRACTION83
2.821-2.9340.29531550.23743809X-RAY DIFFRACTION98
2.934-3.06750.30751600.23253899X-RAY DIFFRACTION100
3.0675-3.22920.23931610.22813901X-RAY DIFFRACTION100
3.2292-3.43140.24761600.21173883X-RAY DIFFRACTION100
3.4314-3.69630.24831630.19613955X-RAY DIFFRACTION100
3.6963-4.0680.21631620.17883932X-RAY DIFFRACTION100
4.068-4.65620.22011630.16183974X-RAY DIFFRACTION100
4.6562-5.86450.21751650.18364002X-RAY DIFFRACTION100
5.8645-46.39110.22861720.2044148X-RAY DIFFRACTION99
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)
12.2468-0.02490.30193.932-0.61115.31320.1607-0.13490.0678-0.0598-0.10621.9915-0.1966-1.3233-0.20380.24320.0326-0.05680.47080.00830.6215-65.6435-13.7217-10.2477
24.89370.14480.86854.6175-0.34644.7954-0.22930.01840.132-0.72910.07870.0263-0.0238-0.07540.10850.23070.01860.010.1590.01220.1047-51.1942-8.6691-13.8397
31.3893-0.43680.70071.0473-2.04833.89590.08990.6777-0.1886-0.1237-0.22840.2376-0.50771.03930.15050.8446-0.0822-0.10070.6693-0.10490.3736-48.9804-7.7331-37.7718
42.96450.7132-2.04931.3954-0.70344.39160.16450.21770.5366-0.0221-0.1542-0.537-0.80370.7212-0.42060.1535-0.0451-0.00010.46020.03910.5109-32.4269-4.36934.1486
55.45364.37462.88737.03333.50996.0729-0.04280.01650.6295-0.3176-0.22870.0714-0.65360.26880.24070.21670.0076-0.00880.14580.04190.2812-41.7315-3.0647-0.4748
66.21374.2817-6.70054.8674-4.5117.2492-0.67580.831-0.5881-0.38850.37320.01431.0274-0.68410.49320.21570.03740.05530.4698-0.05290.2879-43.336-14.8541-6.1835
72.5311-1.63041.1757.54852.47912.24430.10130.2634-0.1147-0.1941-0.10330.06880.29310.33040.01440.08410.06710.01570.2376-0.02280.2232-37.3128-14.0752.2479
82.63660.5701-2.21631.47190.42892.64210.03570.24010.1033-0.30580.3147-0.4382-0.08640.818-0.90.760.3060.63411.24-0.00270.5069-26.3349-10.6565-18.7039
91.5476-0.1576-0.26982.40251.36657.07710.21690.4742-0.1918-0.3317-0.3977-0.63520.38310.46180.21470.33620.28780.02420.3562-0.05130.5073-30.7233-21.37453.8298
104.9149-2.0815-2.73785.62880.70983.4031-0.4025-0.4721-0.04760.77180.189-1.0470.11281.2996-0.45140.18550.1156-0.08330.5040.03720.487-28.0479-11.598214.2019
111.10840.98450.52411.1417-0.2131.9717-0.08850.2976-0.4658-0.3295-0.1905-0.61380.3710.45780.340.17450.24650.22960.9436-0.23180.7115-23.9914-21.2833-5.9283
121.9771-0.79151.20053.3415-0.86972.4181-0.4586-0.46720.11610.39750.20960.1698-0.4632-0.2934-0.5730.81090.385-0.26080.24490.0080.4171-60.14239.4415-3.5727
134.0932-0.60191.13391.074-1.09281.2269-0.12-0.2038-0.00210.34670.04320.9389-0.5584-0.9127-0.0720.31960.2304-0.02420.4867-0.04350.5682-60.72942.2213-3.0544
145.9037-3.82093.66182.6732-3.17985.6535-0.14090.05070.60830.03010.03230.9182-0.8437-0.92540.18740.66690.2623-0.19610.55040.07750.8622-65.21217.4738-10.9779
151.9327-1.5295-0.23665.2531.64220.5738-0.4882-0.24190.33710.44250.1978-0.4303-0.9578-0.20.09980.77390.1332-0.18280.28910.06140.4325-49.960512.5692-4.265
161.4745-2.2645-2.1044.14124.57695.76830.0528-0.15880.46830.39650.2739-0.6814-1.00980.3353-0.41411.16160.0155-0.28270.33750.01370.6467-48.359320.5474-5.0939
176.4669-2.6151-3.22691.0581.30521.6102-0.2241.71121.4377-2.4901-0.6976-0.0324-0.5546-0.2350.70921.42590.2747-0.18830.67540.17270.6939-54.278319.7937-19.7019
181.48490.302-0.47756.4671.18420.4140.0241-0.37830.49970.94690.24360.0745-0.5248-0.0934-0.19371.5270.4275-0.26750.357-0.04160.7436-59.023426.57841.0841
198.5386-2.7929-0.114.2848-0.77582.2161-0.9392-1.1720.13711.21440.56120.2847-0.3916-0.0953-0.15421.43430.5755-0.29530.6609-0.0510.7303-63.289921.8798-0.5844
203.7667-2.1027-0.61254.1087-1.15211.61860.0921-0.11650.53240.27910.42880.3591-0.3122-0.4029-0.40060.93230.5379-0.32590.5172-0.00121.0855-67.720416.6481-9.793
216.52264.01165.0575.71724.02415.66510.527-0.2234-0.1893-0.0196-0.68871.7656-0.127-1.31380.13320.64790.31060.15811.96670.32241.1224-66.878411.545938.3891
224.4749-0.009-1.09947.6857-1.08377.0620.06670.27820.10890.26380.39750.2958-0.1786-1.6687-0.40820.52230.0311-0.01960.62880.05370.2038-52.43038.144647.5307
235.8823-4.68316.18354.634-6.06997.9525-0.27851.42940.50881.61010.1987-0.188-2.0092-0.6710.01261.20090.40670.1371.00150.37151.0335-53.069424.914146.1602
241.05020.0208-0.73590.5346-1.96927.6249-0.00730.06420.0296-0.23890.0471-0.15780.4495-0.6393-0.04270.8583-0.04860.2020.4313-0.12440.4389-52.84594.584767.1658
253.29420.31751.58673.8754.59495.9109-0.21590.19860.5734-1.27490.136-0.7471-0.23220.6718-0.12920.7174-0.03710.29180.43970.01330.3982-42.64313.59778.5561
263.4439-1.0531.25423.24790.98084.9110.233-0.23460.25650.0282-0.1934-0.6146-0.53310.0296-0.01850.3273-0.20440.06990.34450.01080.3142-34.76758.854130.4774
276.9837-0.95633.07186.14270.09455.8555-0.06770.4687-0.66050.64160.7285-1.12140.6051.1363-0.56720.41830.029-0.0310.4145-0.15060.4907-31.85272.503727.087
285.3738-5.0904-4.81045.03314.30394.741-0.3001-0.269-0.32140.72350.43630.32980.8311-0.5374-0.12150.5351-0.0368-0.05490.47720.03470.3729-41.94973.690533.8622
296.41372.41090.73222.1763-3.08368.9883-0.1464-0.16921.09050.83580.5440.1142-2.2694-1.2395-0.10330.88350.03160.11770.5393-0.07110.4157-44.190315.431739.5553
305.48991.0513-2.44777.78333.2162.87980.4864-0.19150.6115-0.02370.0650.0219-0.8264-0.0065-0.32860.559-0.10510.13730.1986-0.0060.3374-38.26514.933731.1166
314.3261-0.12633.21473.4144-0.50912.94520.214-0.47-0.14910.69580.2524-0.90950.15640.5742-0.83830.8423-0.4101-0.39451.3307-0.28210.7347-27.260312.112652.1676
321.53590.2948-1.11764.13.55875.44810.9196-0.9998-0.4811.8158-0.3482-0.91760.29570.4893-0.50681.3369-0.6319-0.19330.7243-0.05810.6508-29.951422.450446.043
330.2076-0.03710.0530.30110.07560.37330.0654-0.14630.35660.2029-0.144-0.0581-0.30690.0884-0.64991.4065-0.44020.30740.37-0.08020.7773-32.804722.642224.8758
343.38312.16912.82486.36381.63015.2290.05840.3399-0.0712-0.70080.4369-1.0604-0.76821.37050.02070.6814-0.31790.27580.5078-0.10270.6787-28.912613.085419.0576
355.0683-2.55040.76367.3929-3.48373.1881-0.5666-0.62731.94540.68530.1409-1.4452-0.93070.32830.42541.047-0.5425-0.07450.8302-0.3090.9196-25.311822.94139.3583
360.1290.4021-0.18771.2047-0.56380.2569-0.37220.491-0.1385-0.07510.02030.73471.933-2.69360.23781.3451-0.79660.12231.7032-0.14180.7993-59.0139-5.949835.1478
370.0051-0.17930.05765.5538-1.74160.54580.4133-0.27150.28010.684-0.07731.2270.399-1.308-0.05771.1904-1.02660.04832.2324-0.04580.6267-66.8082-5.770642.0793
381.02420.55110.26730.39050.19230.1072-0.33660.1472-0.78260.20260.08750.01342.3017-1.21360.41042.2458-0.70540.28170.991-0.09820.7304-51.9123-15.103239.6619
392.8999-0.45160.47370.6444-0.55970.49140.7785-0.3265-0.91171.518-0.60580.79352.0333-1.1346-0.29072.3002-0.8583-0.06271.3473-0.12651.1523-60.3922-26.827532.8743
407.81944.4319-1.61535.9108-0.54360.3746-0.12690.50970.1914-0.20560.30720.20430.1369-0.3196-0.05472.0033-1.24180.10351.90990.04131.3098-67.5169-16.491344.8991
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 199 through 229 )
2X-RAY DIFFRACTION2chain 'A' and (resid 230 through 295 )
3X-RAY DIFFRACTION3chain 'A' and (resid 296 through 353 )
4X-RAY DIFFRACTION4chain 'B' and (resid 12 through 94 )
5X-RAY DIFFRACTION5chain 'B' and (resid 95 through 118 )
6X-RAY DIFFRACTION6chain 'B' and (resid 119 through 131 )
7X-RAY DIFFRACTION7chain 'B' and (resid 132 through 150 )
8X-RAY DIFFRACTION8chain 'B' and (resid 151 through 186 )
9X-RAY DIFFRACTION9chain 'B' and (resid 187 through 214 )
10X-RAY DIFFRACTION10chain 'B' and (resid 215 through 241 )
11X-RAY DIFFRACTION11chain 'B' and (resid 242 through 247 )
12X-RAY DIFFRACTION12chain 'C' and (resid 5 through 28 )
13X-RAY DIFFRACTION13chain 'C' and (resid 29 through 52 )
14X-RAY DIFFRACTION14chain 'C' and (resid 53 through 64 )
15X-RAY DIFFRACTION15chain 'C' and (resid 65 through 92 )
16X-RAY DIFFRACTION16chain 'C' and (resid 93 through 110 )
17X-RAY DIFFRACTION17chain 'C' and (resid 111 through 118 )
18X-RAY DIFFRACTION18chain 'C' and (resid 119 through 147 )
19X-RAY DIFFRACTION19chain 'C' and (resid 148 through 161 )
20X-RAY DIFFRACTION20chain 'C' and (resid 162 through 178 )
21X-RAY DIFFRACTION21chain 'D' and (resid 211 through 220 )
22X-RAY DIFFRACTION22chain 'D' and (resid 221 through 290 )
23X-RAY DIFFRACTION23chain 'D' and (resid 291 through 295 )
24X-RAY DIFFRACTION24chain 'D' and (resid 296 through 331 )
25X-RAY DIFFRACTION25chain 'D' and (resid 332 through 353 )
26X-RAY DIFFRACTION26chain 'E' and (resid 13 through 30 )
27X-RAY DIFFRACTION27chain 'E' and (resid 31 through 94 )
28X-RAY DIFFRACTION28chain 'E' and (resid 95 through 118 )
29X-RAY DIFFRACTION29chain 'E' and (resid 119 through 131 )
30X-RAY DIFFRACTION30chain 'E' and (resid 132 through 150 )
31X-RAY DIFFRACTION31chain 'E' and (resid 151 through 186 )
32X-RAY DIFFRACTION32chain 'E' and (resid 187 through 192 )
33X-RAY DIFFRACTION33chain 'E' and (resid 193 through 214 )
34X-RAY DIFFRACTION34chain 'E' and (resid 215 through 241 )
35X-RAY DIFFRACTION35chain 'E' and (resid 242 through 247 )
36X-RAY DIFFRACTION36chain 'F' and (resid 6 through 42 )
37X-RAY DIFFRACTION37chain 'F' and (resid 43 through 56 )
38X-RAY DIFFRACTION38chain 'F' and (resid 57 through 125 )
39X-RAY DIFFRACTION39chain 'F' and (resid 126 through 163 )
40X-RAY DIFFRACTION40chain 'F' and (resid 164 through 178 )

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