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- PDB-5m5v: Clathrin heavy chain N-terminal domain bound to a clathrin-box mo... -

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Basic information

Entry
Database: PDB / ID: 5m5v
TitleClathrin heavy chain N-terminal domain bound to a clathrin-box motif from hepatitis D virus large antigen (clade 2)
Components
  • Clathrin heavy chain 1
  • Large delta antigen
KeywordsENDOCYTOSIS / hepatitis delta virus / HDAg-L
Function / homology
Function and homology information


Retrograde neurotrophin signalling / Recycling pathway of L1 / WNT5A-dependent internalization of FZD4 / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / LDL clearance / Gap junction degradation / Formation of annular gap junctions / Golgi Associated Vesicle Biogenesis / RHOU GTPase cycle / RHOV GTPase cycle ...Retrograde neurotrophin signalling / Recycling pathway of L1 / WNT5A-dependent internalization of FZD4 / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / LDL clearance / Gap junction degradation / Formation of annular gap junctions / Golgi Associated Vesicle Biogenesis / RHOU GTPase cycle / RHOV GTPase cycle / clathrin coat of trans-Golgi network vesicle / Lysosome Vesicle Biogenesis / clathrin light chain binding / negative regulation of hyaluronan biosynthetic process / clathrin complex / MHC class II antigen presentation / VLDLR internalisation and degradation / clathrin coat of coated pit / Cargo recognition for clathrin-mediated endocytosis / clathrin coat disassembly / clathrin coat assembly / clathrin-coated endocytic vesicle / membrane coat / Clathrin-mediated endocytosis / arrestin family protein binding / receptor-mediated endocytosis / intracellular protein transport / autophagy / spindle / viral penetration into host nucleus / host cell / disordered domain specific binding / melanosome / mitotic cell cycle / symbiont entry into host cell / protein domain specific binding / cell division / structural molecule activity / mitochondrion / RNA binding / extracellular exosome / identical protein binding
Similarity search - Function
Hepatitis delta virus delta antigen / Delta antigen, N-terminal / Hepatitis delta virus delta antigen / Clathrin heavy-chain terminal domain / Hepatitis delta antigen (HDAg) domain / Hepatitis delta antigen (HDAg) domain profile. / Clathrin-H-link / Clathrin, heavy chain, linker, core motif / Clathrin heavy chain, N-terminal / Clathrin, heavy chain ...Hepatitis delta virus delta antigen / Delta antigen, N-terminal / Hepatitis delta virus delta antigen / Clathrin heavy-chain terminal domain / Hepatitis delta antigen (HDAg) domain / Hepatitis delta antigen (HDAg) domain profile. / Clathrin-H-link / Clathrin, heavy chain, linker, core motif / Clathrin heavy chain, N-terminal / Clathrin, heavy chain / Clathrin, heavy chain, propeller repeat / Clathrin propeller repeat / Clathrin, heavy-chain linker / Region in Clathrin and VPS / Clathrin heavy chain repeat homology / Clathrin, heavy chain/VPS, 7-fold repeat / Clathrin heavy-chain (CHCR) repeat profile. / 7 Propeller / Methylamine Dehydrogenase; Chain H / Tetratricopeptide-like helical domain superfamily / Armadillo-type fold / Mainly Beta
Similarity search - Domain/homology
Large delta antigen / Clathrin heavy chain 1
Similarity search - Component
Biological speciesBos taurus (cattle)
Hepatitis delta virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsMuenzner, J. / Graham, S.C.
Funding support United Kingdom, United States, 3items
OrganizationGrant numberCountry
Wellcome Trust and Royal Society098406/Z/12/Z United Kingdom
Wellcome Trust090909/Z/09/Z United Kingdom
National Institutes of HealthGM106963 United States
CitationJournal: Traffic / Year: 2017
Title: Cellular and viral peptides bind multiple sites on the N-terminal domain of clathrin.
Authors: Muenzner, J. / Traub, L.M. / Kelly, B.T. / Graham, S.C.
History
DepositionOct 22, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 23, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2017Group: Database references
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Clathrin heavy chain 1
B: Clathrin heavy chain 1
E: Large delta antigen
F: Large delta antigen
G: Large delta antigen
H: Large delta antigen
I: Large delta antigen
J: Large delta antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,2469
Polymers87,1548
Non-polymers921
Water10,503583
1
A: Clathrin heavy chain 1
E: Large delta antigen
G: Large delta antigen
I: Large delta antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,6695
Polymers43,5774
Non-polymers921
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2510 Å2
ΔGint-18 kcal/mol
Surface area16500 Å2
MethodPISA
2
B: Clathrin heavy chain 1
F: Large delta antigen
H: Large delta antigen
J: Large delta antigen


Theoretical massNumber of molelcules
Total (without water)43,5774
Polymers43,5774
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2300 Å2
ΔGint-18 kcal/mol
Surface area16410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.900, 131.230, 78.450
Angle α, β, γ (deg.)90.00, 115.86, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-748-

HOH

21A-762-

HOH

31B-536-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ILE / Beg label comp-ID: ILE / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _ / Auth seq-ID: 4 - 363 / Label seq-ID: 6 - 365

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Antibody Clathrin heavy chain 1


Mass: 40540.473 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: N-terminal residues 'GS' are residual following cleavage of the purification tag
Source: (gene. exp.) Bos taurus (cattle) / Gene: CLTC / Plasmid: pOPT3G / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: P49951
#2: Protein/peptide
Large delta antigen


Mass: 1012.181 Da / Num. of mol.: 6 / Fragment: Clathrin-box like motif, UNP Residues 203-209 / Source method: obtained synthetically
Details: N- and C-terminal serine residues are non-natural and were added to enhance solubility
Source: (synth.) Hepatitis delta virus / References: UniProt: A4ZNG7
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 583 / Source method: isolated from a natural source / Formula: H2O

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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: 3.64 Å3/Da / Density % sol: 66.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 200 nL protein:peptide (20 mg/mL NTD and 3.6 mM peptide) plus 400 nL reservoir equilibrated against a 80 uL reservoir of 1.75 M sodium malonate pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 7, 2013 / Details: KB mirrors
RadiationMonochromator: Si(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.96→39.2 Å / Num. obs: 79976 / % possible obs: 94.6 % / Redundancy: 2.5 % / CC1/2: 0.996 / Rmerge(I) obs: 0.081 / Net I/σ(I): 7.2
Reflection shellResolution: 1.96→2 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.581 / Mean I/σ(I) obs: 1.5 / CC1/2: 0.563 / % possible all: 95.9

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
iMOSFLMdata reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1C9I

1c9i


Resolution: 1.96→39.2 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.958 / SU B: 5.697 / SU ML: 0.082 / Cross valid method: THROUGHOUT / ESU R: 0.119 / ESU R Free: 0.112 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19343 4224 5 %RANDOM
Rwork0.16914 ---
obs0.17037 79976 94.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 33.338 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å2-0 Å2-0.51 Å2
2--0.21 Å20 Å2
3---0.02 Å2
Refinement stepCycle: 1 / Resolution: 1.96→39.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5862 0 6 583 6451
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0195999
X-RAY DIFFRACTIONr_bond_other_d0.0060.025850
X-RAY DIFFRACTIONr_angle_refined_deg1.9171.968135
X-RAY DIFFRACTIONr_angle_other_deg1.096313464
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2335748
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.26325260
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.112151044
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3921528
X-RAY DIFFRACTIONr_chiral_restr0.120.2933
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0216762
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021326
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_it1.7671.5283010
X-RAY DIFFRACTIONr_mcbond_other1.7671.5273009
X-RAY DIFFRACTIONr_mcangle_it2.8052.2633752
X-RAY DIFFRACTIONr_mcangle_other2.8052.2643753
X-RAY DIFFRACTIONr_scbond_it2.4941.812989
X-RAY DIFFRACTIONr_scbond_other2.4941.8112990
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.9072.6094384
X-RAY DIFFRACTIONr_long_range_B_refined8.24613.5726846
X-RAY DIFFRACTIONr_long_range_B_other8.24513.5786847
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 23170 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.05 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.96→2.011 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 279 -
Rwork0.289 6057 -
obs--95.8 %
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)
11.58860.27670.79921.5490.87752.14590.0448-0.15860.16320.05030.0358-0.14270.04160.1861-0.08060.0542-0.0061-0.01230.0872-0.03690.043619.2550.43318.013
22.62950.63580.03651.4495-0.38351.34540.04470.10520.094-0.17680.0470.14150.1903-0.1591-0.09160.163-0.0335-0.05550.05510.01080.027712.84319.98358.511
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 363
2X-RAY DIFFRACTION2B4 - 363

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