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- PDB-2gd5: Structural basis for budding by the ESCRTIII factor CHMP3 -

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Basic information

Entry
Database: PDB / ID: 2gd5
TitleStructural basis for budding by the ESCRTIII factor CHMP3
ComponentsCharged multivesicular body protein 3
KeywordsPROTEIN TRANSPORT / CHMP3 / ESCRT-III
Function / homology
Function and homology information


regulation of endosome size / multivesicular body-lysosome fusion / amphisome membrane / vesicle fusion with vacuole / suppression of viral release by host / late endosome to lysosome transport / ESCRT III complex / kinetochore microtubule / endosome transport via multivesicular body sorting pathway / regulation of centrosome duplication ...regulation of endosome size / multivesicular body-lysosome fusion / amphisome membrane / vesicle fusion with vacuole / suppression of viral release by host / late endosome to lysosome transport / ESCRT III complex / kinetochore microtubule / endosome transport via multivesicular body sorting pathway / regulation of centrosome duplication / nuclear membrane reassembly / Sealing of the nuclear envelope (NE) by ESCRT-III / midbody abscission / multivesicular body sorting pathway / plasma membrane repair / membrane fission / phosphatidylcholine binding / late endosome to vacuole transport / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / multivesicular body membrane / multivesicular body assembly / regulation of mitotic spindle assembly / Translation of Replicase and Assembly of the Replication Transcription Complex / regulation of early endosome to late endosome transport / mitotic metaphase chromosome alignment / molecular function inhibitor activity / nucleus organization / Macroautophagy / ubiquitin-specific protease binding / viral budding via host ESCRT complex / positive regulation of cytokinesis / viral release from host cell / autophagosome membrane / autophagosome maturation / protein polymerization / Pyroptosis / nuclear pore / phosphatidylinositol-4,5-bisphosphate binding / Endosomal Sorting Complex Required For Transport (ESCRT) / multivesicular body / viral budding from plasma membrane / HCMV Late Events / macroautophagy / Late endosomal microautophagy / Budding and maturation of HIV virion / kinetochore / autophagy / protein transport / late endosome / Translation of Replicase and Assembly of the Replication Transcription Complex / midbody / cytoplasmic vesicle / early endosome / lysosomal membrane / apoptotic process / extracellular exosome / identical protein binding / plasma membrane / cytosol
Similarity search - Function
Helix Hairpins - #1230 / Snf7 family / Snf7 / Helix Hairpins / Helix non-globular / Special
Similarity search - Domain/homology
Charged multivesicular body protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å
AuthorsMuziol, T.M. / Pineda-Molina, E. / Ravelli, R.B. / Zamborlini, A. / Usami, Y. / Gottlinger, H. / Weissenhorn, W.
CitationJournal: Dev.Cell / Year: 2006
Title: Structural Basis for Budding by the ESCRT-III Factor CHMP3.
Authors: Pineda-Molina, E. / Ravelli, R.B. / Zamborlini, A. / Usami, Y. / Weissenhorn, W.
History
DepositionMar 15, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Charged multivesicular body protein 3
B: Charged multivesicular body protein 3
C: Charged multivesicular body protein 3
D: Charged multivesicular body protein 3


Theoretical massNumber of molelcules
Total (without water)84,0064
Polymers84,0064
Non-polymers00
Water00
1
A: Charged multivesicular body protein 3
B: Charged multivesicular body protein 3


Theoretical massNumber of molelcules
Total (without water)42,0032
Polymers42,0032
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3550 Å2
ΔGint-24 kcal/mol
Surface area17420 Å2
MethodPISA
2
C: Charged multivesicular body protein 3
D: Charged multivesicular body protein 3


Theoretical massNumber of molelcules
Total (without water)42,0032
Polymers42,0032
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3400 Å2
ΔGint-26 kcal/mol
Surface area17830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.580, 72.570, 89.230
Angle α, β, γ (deg.)68.68, 83.61, 76.70
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
12A
22B
32C
42D
13A
23B
33C
43D

NCS domain segments:

Component-ID: 1 / Refine code: 6

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11VALVALGLNGLNAA16 - 9412 - 90
21VALVALGLNGLNBB16 - 9412 - 90
31VALVALGLNGLNCC16 - 9412 - 90
41VALVALGLNGLNDD16 - 9412 - 90
12GLUGLUVALVALAA109 - 118105 - 114
22GLUGLUVALVALBB109 - 118105 - 114
32GLUGLUVALVALCC109 - 118105 - 114
42GLUGLUVALVALDD109 - 118105 - 114
13MSEMSEMSEMSEAA127 - 134123 - 130
23MSEMSEMSEMSEBB127 - 134123 - 130
33MSEMSEMSEMSECC127 - 134123 - 130
43MSEMSEMSEMSEDD127 - 134123 - 130

NCS ensembles :
ID
1
2
3

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Components

#1: Protein
Charged multivesicular body protein 3 / Chromatin-modifying protein 3 / Vacuolar protein sorting 24 / hVps24 / Neuroendocrine differentiation factor


Mass: 21001.621 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CHMP3 / Plasmid: pProExHtb / Production host: Escherichia coli (E. coli) / Strain (production host): BL 21 codon + / References: UniProt: Q9Y3E7
Has protein modificationY

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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: 2.35 Å3/Da / Density % sol: 47.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 8-12% PEG 3350, 200mM ammonium acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.97927 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Jan 31, 2005
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97927 Å / Relative weight: 1
ReflectionResolution: 2.8→33 Å / Num. obs: 17853 / % possible obs: 94.7 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 63.075 Å2 / Rmerge(I) obs: 0.096 / Net I/σ(I): 14.33
Reflection shellResolution: 2.8→3 Å / Rmerge(I) obs: 0.464 / Mean I/σ(I) obs: 4.98 / % possible all: 94.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
ProDCdata collection
XDSdata scaling
SHELXSphasing
RefinementMethod to determine structure: SAD / Resolution: 2.8→20 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.907 / SU B: 42.655 / SU ML: 0.38 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.461 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.30106 909 5.1 %RANDOM
Rwork0.25883 ---
obs0.26106 16944 95.68 %-
all-18713 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 59.707 Å2
Baniso -1Baniso -2Baniso -3
1-4.86 Å21.09 Å20.25 Å2
2---5.72 Å2-2.36 Å2
3---2.02 Å2
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4746 0 0 0 4746
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0224772
X-RAY DIFFRACTIONr_angle_refined_deg1.5111.9986329
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5835593
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.6124.396182
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.328151114
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.931543
X-RAY DIFFRACTIONr_chiral_restr0.0870.2735
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023255
X-RAY DIFFRACTIONr_nbd_refined0.3030.22560
X-RAY DIFFRACTIONr_nbtor_refined0.3210.23351
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.2204
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3010.277
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0440.21
X-RAY DIFFRACTIONr_mcbond_it1.0141.53124
X-RAY DIFFRACTIONr_mcangle_it1.57724810
X-RAY DIFFRACTIONr_scbond_it2.40831874
X-RAY DIFFRACTIONr_scangle_it3.8294.51519
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A642loose positional0.195
12B642loose positional0.225
13C642loose positional0.275
14D642loose positional0.255
21A76loose positional0.25
22B76loose positional0.225
23C76loose positional0.235
24D76loose positional0.185
31A68loose positional0.265
32B68loose positional0.295
33C68loose positional0.295
34D68loose positional0.35
11A642loose thermal4.310
12B642loose thermal5.310
13C642loose thermal7.4710
14D642loose thermal6.1310
21A76loose thermal2.2110
22B76loose thermal3.8910
23C76loose thermal4.3610
24D76loose thermal5.8310
31A68loose thermal3.7310
32B68loose thermal6.1710
33C68loose thermal7.1210
34D68loose thermal7.3110
LS refinement shellResolution: 2.8→2.871 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.516 57 -
Rwork0.372 1144 -
obs--93.32 %
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)
10.3811-1.3862-0.35335.95832.43211.7632-0.0318-0.15-0.0446-0.29430.26370.24390.03280.1653-0.23190.04080.06050.10670.00690.07770.055310.950928.303863.9954
20.5284-1.8184-0.62737.56841.73260.88280.1405-0.0658-0.1465-0.418-0.07510.43090.00040.0275-0.06540.04560.1041-0.1136-0.00010.0106-0.034611.434120.398479.4043
30.69162.22630.95297.16623.07372.63630.11490.0641-0.01120.4074-0.0618-0.0126-0.00190.1428-0.05310.0136-0.098-0.03810.03570.0541-0.049617.399130.123736.0864
40.30981.15180.41784.96551.04270.94410.07510.11260.04140.2617-0.06550.12540.03220.0734-0.0096-0.0816-0.02980.03940.01880.02640.045417.185441.173521.6784
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA12 - 1418 - 137
2X-RAY DIFFRACTION1AA161 - 171157 - 167
3X-RAY DIFFRACTION2BB5 - 1401 - 136
4X-RAY DIFFRACTION2BB161 - 180157 - 176
5X-RAY DIFFRACTION3CC12 - 988 - 94
6X-RAY DIFFRACTION3CC102 - 14098 - 136
7X-RAY DIFFRACTION4DD5 - 1411 - 137
8X-RAY DIFFRACTION4DD157 - 181153 - 177

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