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- PDB-4atm: Crystal structure of the BAR domain of human Amphiphysin, isoform... -

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Basic information

Entry
Database: PDB / ID: 4atm
TitleCrystal structure of the BAR domain of human Amphiphysin, isoform 1 at 1.8 Angstrom resolution featuring increased order at the N- terminus.
ComponentsAMPHIPHYSIN
KeywordsSTRUCTURAL PROTEIN / INVAGINATION / KNOBS-IN-HOLES / STRUCTURAL GENOMICS CONSORTIUM / SGC
Function / homology
Function and homology information


leading edge membrane / synaptic vesicle endocytosis / phospholipid binding / synaptic vesicle membrane / endocytosis / synaptic vesicle / actin cytoskeleton / Clathrin-mediated endocytosis / chemical synaptic transmission / plasma membrane / cytosol
Similarity search - Function
Amphiphysin, isoform 1 / Amphiphysin I, SH3 domain / Amphiphysin / BAR domain / BAR domain profile. / BAR / Arfaptin homology (AH) domain/BAR domain / BAR domain / AH/BAR domain superfamily / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 ...Amphiphysin, isoform 1 / Amphiphysin I, SH3 domain / Amphiphysin / BAR domain / BAR domain profile. / BAR / Arfaptin homology (AH) domain/BAR domain / BAR domain / AH/BAR domain superfamily / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.783 Å
AuthorsAllerston, C.K. / Krojer, T. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. / Bountra, C. / von Delft, F. / Gileadi, O.
CitationJournal: To be Published
Title: Crystal Structure of the Bar Domain of Human Amphiphysin, Isoform 1
Authors: Allerston, C.K. / Krojer, T. / Gileadi, O.
History
DepositionMay 8, 2012Deposition site: PDBE / Processing site: PDBE
SupersessionMay 30, 2012ID: 4A3A
Revision 1.0May 30, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 5, 2012Group: Structure summary
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: AMPHIPHYSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0408
Polymers28,5451
Non-polymers4957
Water4,197233
1
A: AMPHIPHYSIN
hetero molecules

A: AMPHIPHYSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,08016
Polymers57,0912
Non-polymers98914
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-1/31
Buried area7000 Å2
ΔGint-27.3 kcal/mol
Surface area22830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.390, 82.390, 86.590
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-2037-

HOH

21A-2082-

HOH

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Components

#1: Protein AMPHIPHYSIN /


Mass: 28545.377 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-242
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3-PRARE2 / References: UniProt: P49418
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 233 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsG116E MUTATION DERIVED DURING PCR

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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: 2.99 Å3/Da / Density % sol: 58.82 % / Description: NONE
Crystal growpH: 7 / Details: 20% PEG 3350, 0.1 M CITRATE PH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 21, 2011 / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.78→37.2 Å / Num. obs: 32882 / % possible obs: 100 % / Redundancy: 7.6 % / Biso Wilson estimate: 25.89 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 12.8
Reflection shellResolution: 1.78→1.88 Å / Redundancy: 7.9 % / Rmerge(I) obs: 0.97 / Mean I/σ(I) obs: 2.2 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.7.3_928)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3SOG

3sog


Resolution: 1.783→37.014 Å / SU ML: 0.22 / σ(F): 1.33 / Phase error: 20.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2181 1668 5.1 %
Rwork0.1872 --
obs0.1887 32833 99.92 %
Solvent computationShrinkage radii: 1.11 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.719 Å2 / ksol: 0.323 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.9932 Å20 Å20 Å2
2--2.9932 Å20 Å2
3----5.9864 Å2
Refinement stepCycle: LAST / Resolution: 1.783→37.014 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1784 0 32 233 2049
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071911
X-RAY DIFFRACTIONf_angle_d0.942574
X-RAY DIFFRACTIONf_dihedral_angle_d13.61734
X-RAY DIFFRACTIONf_chiral_restr0.066276
X-RAY DIFFRACTIONf_plane_restr0.004334
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.783-1.83550.31361600.28622548X-RAY DIFFRACTION100
1.8355-1.89480.29321220.26692568X-RAY DIFFRACTION100
1.8948-1.96250.28651370.25152583X-RAY DIFFRACTION100
1.9625-2.0410.26151420.22112534X-RAY DIFFRACTION100
2.041-2.13390.23661380.19482595X-RAY DIFFRACTION100
2.1339-2.24640.2051390.1842561X-RAY DIFFRACTION100
2.2464-2.38710.18891330.17072598X-RAY DIFFRACTION100
2.3871-2.57140.20981220.17662602X-RAY DIFFRACTION100
2.5714-2.83010.22481500.19052579X-RAY DIFFRACTION100
2.8301-3.23940.21771630.17032596X-RAY DIFFRACTION100
3.2394-4.08050.19651280.17192656X-RAY DIFFRACTION100
4.0805-37.02190.20251340.18052745X-RAY DIFFRACTION100
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)
10.3873-0.81871.12721.7341-2.3863.28151.068-3.5130.02883.699-0.2832-1.29311.27142.0288-0.76021.2090.1407-0.2941.1137-0.29480.638239.11564.654644.9498
23.56073.00365.63332.9445.11069.209-0.1721-0.12920.1546-0.2319-0.05430.1109-0.4673-0.28090.28780.17010.00610.00460.1848-0.00730.208819.6992-14.12264.2181
32.20221.31632.34142.95512.96758.10580.2006-0.0459-0.03770.2279-0.20330.20970.7103-0.69750.02370.0634-0.0262-0.00830.21450.00110.24774.9573-36.0251-16.3183
40.39452.63833.22465.86216.78476.23160.0405-0.33340.2354-0.026-0.52140.3285-0.0449-1.01450.47920.2760.00130.01470.3224-0.12550.285121.4062-4.15425.1132
50.34460.83951.31993.48014.29426.03590.125-0.05190.0380.5225-0.10420.01890.5442-0.19540.00630.1291-0.04610.05290.1205-0.01460.199620.9501-19.46689.9799
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 19:23)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 24:84)
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 85:116)
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 117:157)
5X-RAY DIFFRACTION5CHAIN A AND (RESSEQ 158:239)

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