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- PDB-4abm: Crystal Structure of CHMP4B hairpin -

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Basic information

Entry
Database: PDB / ID: 4abm
TitleCrystal Structure of CHMP4B hairpin
ComponentsCHARGED MULTIVESICULAR BODY PROTEIN 4B
KeywordsPROTEIN TRANSPORT / CELL CYCLE / HIV-1
Function / homology
Function and homology information


ubiquitin-independent protein catabolic process via the multivesicular body sorting pathway / maintenance of lens transparency / amphisome membrane / multivesicular body-lysosome fusion / viral budding / vesicle fusion with vacuole / late endosome to lysosome transport / ESCRT III complex / kinetochore microtubule / late endosome to vacuole transport via multivesicular body sorting pathway ...ubiquitin-independent protein catabolic process via the multivesicular body sorting pathway / maintenance of lens transparency / amphisome membrane / multivesicular body-lysosome fusion / viral budding / vesicle fusion with vacuole / late endosome to lysosome transport / ESCRT III complex / kinetochore microtubule / late endosome to vacuole 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 / vesicle budding from membrane / membrane coat / post-translational protein targeting to endoplasmic reticulum membrane / membrane fission / plasma membrane repair / multivesicular body membrane / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / multivesicular body assembly / regulation of mitotic spindle assembly / Translation of Replicase and Assembly of the Replication Transcription Complex / nervous system process / exit from mitosis / mitotic metaphase chromosome alignment / Macroautophagy / nucleus organization / viral budding via host ESCRT complex / autophagosome membrane / autophagosome maturation / mitotic cytokinesis / protein polymerization / Pyroptosis / nuclear pore / Endosomal Sorting Complex Required For Transport (ESCRT) / multivesicular body / viral budding from plasma membrane / HCMV Late Events / regulation of autophagy / macroautophagy / Late endosomal microautophagy / Budding and maturation of HIV virion / cytoplasmic side of plasma membrane / kinetochore / autophagy / protein transport / nuclear envelope / Translation of Replicase and Assembly of the Replication Transcription Complex / midbody / vesicle / endosome / cadherin binding / lysosomal membrane / protein homodimerization activity / extracellular exosome / identical protein binding / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
ESAT-6-like / Snf7 family / Snf7 / Helix Hairpins / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Charged multivesicular body protein 4b
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsMartinelli, N. / Hartlieb, B. / Usami, Y. / Sabin, C. / Dordor, A. / Ribeiro, E.A. / Gottlinger, H. / Weissenhorn, W.
CitationJournal: J.Mol.Biol. / Year: 2012
Title: Cc2D1A is a Regulator of Escrt-III Chmp4B.
Authors: Martinelli, N. / Hartlieb, B. / Usami, Y. / Sabin, C. / Dordor, A. / Miguet, N. / Avilov, S.V. / Ribeiro, E.A. / Gottlinger, H. / Weissenhorn, W.
History
DepositionDec 8, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 9, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Source and taxonomy / Category: entity_src_gen / Item: _entity_src_gen.pdbx_host_org_scientific_name
Revision 1.2May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CHARGED MULTIVESICULAR BODY PROTEIN 4B
B: CHARGED MULTIVESICULAR BODY PROTEIN 4B
C: CHARGED MULTIVESICULAR BODY PROTEIN 4B
D: CHARGED MULTIVESICULAR BODY PROTEIN 4B


Theoretical massNumber of molelcules
Total (without water)36,9994
Polymers36,9994
Non-polymers00
Water2,468137
1
A: CHARGED MULTIVESICULAR BODY PROTEIN 4B
B: CHARGED MULTIVESICULAR BODY PROTEIN 4B


Theoretical massNumber of molelcules
Total (without water)18,4992
Polymers18,4992
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1740 Å2
ΔGint-15.7 kcal/mol
Surface area10510 Å2
MethodPISA
2
C: CHARGED MULTIVESICULAR BODY PROTEIN 4B


Theoretical massNumber of molelcules
Total (without water)9,2501
Polymers9,2501
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
D: CHARGED MULTIVESICULAR BODY PROTEIN 4B


Theoretical massNumber of molelcules
Total (without water)9,2501
Polymers9,2501
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.590, 71.430, 123.680
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
CHARGED MULTIVESICULAR BODY PROTEIN 4B / CHROMATIN-MODIFYING PROTEIN 4B / CHMP4B / SNF7 HOMOLOG ASSOCIATED WITH ALIX 1 / SNF7-2 / HSNF7-2 / ...CHROMATIN-MODIFYING PROTEIN 4B / CHMP4B / SNF7 HOMOLOG ASSOCIATED WITH ALIX 1 / SNF7-2 / HSNF7-2 / VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 32-2 / VPS32-2 / HVPS32-2


Mass: 9249.646 Da / Num. of mol.: 4 / Fragment: CHMP4B HAIRPIN, RESIDUES 23-97
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H444
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 137 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsFOUR ADDITIONAL RESIDUES AT THE N-TERMINUS

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.24 Å3/Da / Density % sol: 45.19 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9795
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.8→41.23 Å / Num. obs: 30007 / % possible obs: 99.6 % / Observed criterion σ(I): 4.4 / Redundancy: 7.8 % / Rmerge(I) obs: 0.27 / Net I/σ(I): 16.3
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 4.4 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
iMOSFLMdata scaling
SHELXphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.8→61.86 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.883 / SU B: 6.462 / SU ML: 0.104 / Cross valid method: THROUGHOUT / ESU R: 0.162 / ESU R Free: 0.161 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.28517 1588 5 %RANDOM
Rwork0.22765 ---
obs0.23043 30007 99.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.999 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20 Å2
2--0.06 Å20 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.8→61.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2568 0 0 137 2705
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0192720
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.8841.9883621
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr
X-RAY DIFFRACTIONr_gen_planes_refined
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 123 -
Rwork0.268 1954 -
obs--100 %
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)
11.2866-1.8317-1.37943.15172.03552.84410.10870.09120.1151-0.1247-0.1057-0.0313-0.1468-0.1732-0.0030.02140.00490.00440.0471-0.0250.1086.47841.442512.7617
25.7206-3.2914-1.43222.85131.04460.5842-0.1989-0.1926-0.23490.19130.08410.16010.09440.09440.11480.07030.00310.00680.05370.01030.033618.657617.38759.5986
31.8288-0.73880.7462.213-2.39534.7011-0.00980.1687-0.010.04820.03350.04560.16280.0899-0.02380.0602-0.00050.00120.0604-0.04710.104724.415237.045420.674
41.3112-0.38471.05945.57012.71523.0753-0.0013-0.05790.0393-0.0922-0.15480.1016-0.0329-0.17170.15610.1443-0.04880.06630.0745-0.01160.050211.225121.074825.4593
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 79
2X-RAY DIFFRACTION2B1 - 79
3X-RAY DIFFRACTION3C1 - 78
4X-RAY DIFFRACTION4D3 - 79

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