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- PDB-3a4u: Crystal structure of MCFD2 in complex with carbohydrate recogniti... -

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Basic information

Entry
Database: PDB / ID: 3a4u
TitleCrystal structure of MCFD2 in complex with carbohydrate recognition domain of ERGIC-53
Components
  • Multiple coagulation factor deficiency protein 2
  • Protein ERGIC-53
KeywordsPROTEIN TRANSPORT / LECTIN / ERGIC / ER / GOLGI / TRANSPORT / Disulfide bond / Endoplasmic reticulum / ER-Golgi transport / Golgi apparatus / Membrane / Transmembrane / Disease mutation
Function / homology
Function and homology information


Transport to the Golgi and subsequent modification / positive regulation of organelle organization / negative regulation of protein targeting to mitochondrion / Cargo concentration in the ER / COPII-coated ER to Golgi transport vesicle / endoplasmic reticulum organization / RHOD GTPase cycle / COPII-mediated vesicle transport / RHOC GTPase cycle / endoplasmic reticulum-Golgi intermediate compartment ...Transport to the Golgi and subsequent modification / positive regulation of organelle organization / negative regulation of protein targeting to mitochondrion / Cargo concentration in the ER / COPII-coated ER to Golgi transport vesicle / endoplasmic reticulum organization / RHOD GTPase cycle / COPII-mediated vesicle transport / RHOC GTPase cycle / endoplasmic reticulum-Golgi intermediate compartment / Golgi organization / D-mannose binding / RHOG GTPase cycle / RHOA GTPase cycle / RAC2 GTPase cycle / RAC3 GTPase cycle / endoplasmic reticulum to Golgi vesicle-mediated transport / vesicle-mediated transport / endoplasmic reticulum-Golgi intermediate compartment membrane / sarcomere / ER to Golgi transport vesicle membrane / blood coagulation / unfolded protein binding / protein folding / protein transport / : / Golgi membrane / calcium ion binding / endoplasmic reticulum membrane / endoplasmic reticulum / Golgi apparatus / extracellular exosome / metal ion binding / membrane
Similarity search - Function
: / Legume-like lectin / : / Legume-like lectin family / L-type lectin-like (leguminous) domain profile. / EF-hand / Recoverin; domain 1 / Jelly Rolls - #200 / EF-hand domain pair / EF-Hand 1, calcium-binding site ...: / Legume-like lectin / : / Legume-like lectin family / L-type lectin-like (leguminous) domain profile. / EF-hand / Recoverin; domain 1 / Jelly Rolls - #200 / EF-hand domain pair / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Protein ERGIC-53 / Multiple coagulation factor deficiency protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å
AuthorsNishio, M. / Kamiya, Y. / Mizushima, T. / Wakatsuki, S. / Sasakawa, H. / Yamamoto, K. / Uchiyama, S. / Noda, M. / McKay, A.R. / Fukui, K. ...Nishio, M. / Kamiya, Y. / Mizushima, T. / Wakatsuki, S. / Sasakawa, H. / Yamamoto, K. / Uchiyama, S. / Noda, M. / McKay, A.R. / Fukui, K. / Hauri, H.P. / Kato, K.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Structural basis for the cooperative interplay between the two causative gene products of combined factor V and factor VIII deficiency.
Authors: Nishio, M. / Kamiya, Y. / Mizushima, T. / Wakatsuki, S. / Sasakawa, H. / Yamamoto, K. / Uchiyama, S. / Noda, M. / McKay, A.R. / Fukui, K. / Hauri, H.P. / Kato, K.
History
DepositionJul 17, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 5, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein ERGIC-53
B: Multiple coagulation factor deficiency protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,88510
Polymers44,3562
Non-polymers5298
Water3,405189
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2930 Å2
ΔGint-60 kcal/mol
Surface area13430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.410, 59.410, 198.842
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Protein ERGIC-53 / ER-Golgi intermediate compartment 53 kDa protein / Lectin mannose-binding 1 / Gp58 / Intracellular ...ER-Golgi intermediate compartment 53 kDa protein / Lectin mannose-binding 1 / Gp58 / Intracellular mannose-specific lectin MR60


Mass: 28039.068 Da / Num. of mol.: 1 / Fragment: Carbohydrate Recognition Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LMAN1, ERGIC53, F5F8D / Plasmid: pCold3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 codon plus / References: UniProt: P49257
#2: Protein Multiple coagulation factor deficiency protein 2 / MCFD2 / Neural stem cell-derived neuronal survival protein


Mass: 16316.842 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MCFD2, SDNSF / Plasmid: pET16b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 codon plus / References: UniProt: Q8NI22
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 189 / Source method: isolated from a natural source / Formula: H2O
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: 2.28 Å3/Da / Density % sol: 46.14 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 20% PEG 3350, 0.2M sodium tartrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 13, 2008 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.84→49.81 Å / Num. obs: 36530 / % possible obs: 99.9 % / Redundancy: 6.8 % / Biso Wilson estimate: 19.84 Å2 / Rmerge(I) obs: 0.059 / Rsym value: 0.188 / Net I/σ(I): 19.5
Reflection shellResolution: 1.84→1.94 Å / Redundancy: 7 % / Rmerge(I) obs: 0.257 / Mean I/σ(I) obs: 6.1 / Num. unique all: 5229 / Rsym value: 0.188 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1R1Z

1r1z


Resolution: 1.84→49.81 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.944 / SU B: 1.975 / SU ML: 0.062 / Cross valid method: THROUGHOUT / ESU R: 0.113 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20042 1822 5 %RANDOM
Rwork0.18764 ---
obs0.18828 34626 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.197 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.84→49.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2315 0 28 189 2532
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0222393
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0861.9333237
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.925290
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.13324.882127
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.43115372
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8261511
X-RAY DIFFRACTIONr_chiral_restr0.0770.2335
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021874
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1910.21039
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.21601
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0990.2194
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.070.216
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1630.248
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1470.215
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6441.51487
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.10122318
X-RAY DIFFRACTIONr_scbond_it1.45131034
X-RAY DIFFRACTIONr_scangle_it2.2874.5919
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.838→1.886 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 132 -
Rwork0.231 2469 -
obs--100 %

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