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- PDB-4ygc: Crystal structure of ERGIC-53/MCFD2, monoclinic calcium-bound form 1 -

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Basic information

Entry
Database: PDB / ID: 4ygc
TitleCrystal structure of ERGIC-53/MCFD2, monoclinic calcium-bound form 1
Components
  • Multiple coagulation factor deficiency protein 2
  • Protein ERGIC-53
KeywordsPROTEIN TRANSPORT / BETA-SANDWICH / EF-HAND / CARGO RECEPTOR / CALCIUM BINDING / ER / ERGIC
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 / RHOD GTPase cycle / endoplasmic reticulum organization / COPII-mediated vesicle transport / COPII-coated ER to Golgi transport vesicle / RHOC GTPase cycle / Golgi organization ...Transport to the Golgi and subsequent modification / positive regulation of organelle organization / negative regulation of protein targeting to mitochondrion / Cargo concentration in the ER / RHOD GTPase cycle / endoplasmic reticulum organization / COPII-mediated vesicle transport / COPII-coated ER to Golgi transport vesicle / RHOC GTPase cycle / Golgi organization / mannose binding / RHOG GTPase cycle / RHOA GTPase cycle / endoplasmic reticulum-Golgi intermediate compartment / RAC3 GTPase cycle / RAC2 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 / unfolded protein binding / blood coagulation / protein transport / protein folding / collagen-containing extracellular matrix / Golgi membrane / calcium ion binding / endoplasmic reticulum membrane / Golgi apparatus / endoplasmic reticulum / extracellular exosome / membrane / metal ion binding
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 / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. ...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: 2.4 Å
AuthorsSatoh, T. / Nishio, M. / Yagi-Utsumi, M. / Suzuki, K. / Anzai, T. / Mizushima, T. / Kamiya, Y. / Kato, K.
Funding support Japan, 3items
OrganizationGrant numberCountry
JSPS KAKENHI25121730, 25102008, 24249002 Japan
Okazaki ORION project, Ministry of Education, Culture, Sports, Science and Technology Japan
Nanotechnology Platform Project, Ministry of Education, Culture, Sports, Science and Technology Japan
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2020
Title: Crystallographic snapshots of the EF-hand protein MCFD2 complexed with the intracellular lectin ERGIC-53 involved in glycoprotein transport.
Authors: Satoh, T. / Nishio, M. / Suzuki, K. / Yagi-Utsumi, M. / Kamiya, Y. / Mizushima, T. / Kato, K.
History
DepositionFeb 26, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 6, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2020Group: Data collection / Derived calculations / Category: diffrn_source / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2May 13, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Nov 8, 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 / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_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: Protein ERGIC-53
B: Multiple coagulation factor deficiency protein 2
C: Protein ERGIC-53
D: Multiple coagulation factor deficiency protein 2
E: Protein ERGIC-53
F: Multiple coagulation factor deficiency protein 2
G: Protein ERGIC-53
H: Multiple coagulation factor deficiency protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,62528
Polymers156,8428
Non-polymers78320
Water4,288238
1
A: Protein ERGIC-53
B: Multiple coagulation factor deficiency protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,4067
Polymers39,2102
Non-polymers1965
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2010 Å2
ΔGint-71 kcal/mol
Surface area13360 Å2
MethodPISA
2
C: Protein ERGIC-53
D: Multiple coagulation factor deficiency protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,4067
Polymers39,2102
Non-polymers1965
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2030 Å2
ΔGint-71 kcal/mol
Surface area13370 Å2
MethodPISA
3
E: Protein ERGIC-53
F: Multiple coagulation factor deficiency protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,4067
Polymers39,2102
Non-polymers1965
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2090 Å2
ΔGint-71 kcal/mol
Surface area12510 Å2
MethodPISA
4
G: Protein ERGIC-53
H: Multiple coagulation factor deficiency protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,4067
Polymers39,2102
Non-polymers1965
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1980 Å2
ΔGint-70 kcal/mol
Surface area12870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.616, 168.892, 73.955
Angle α, β, γ (deg.)90.00, 119.86, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12A
22E
13A
23C
14B
24D
15B
25F
16B
26D
17C
27E
18C
28G
19D
29F
110D
210H
111E
211C
112F
212D

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROLEULEUAA42 - 26719 - 244
21PROPROLEULEUCC42 - 26719 - 244
12PROPROLEULEUAA42 - 26719 - 244
22PROPROLEULEUEE42 - 26719 - 244
13PROPROLEULEUAA42 - 26719 - 244
23PROPROLEULEUCC42 - 26719 - 244
14METMETLYSLYSBB67 - 14325 - 101
24METMETLYSLYSDD67 - 14325 - 101
15TYRTYRPHEPHEBB76 - 14134 - 99
25TYRTYRPHEPHEFF76 - 14134 - 99
16GLNGLNALAALABB73 - 14231 - 100
26GLNGLNALAALADD73 - 14231 - 100
17PROPROTHRTHRCC42 - 26819 - 245
27PROPROTHRTHREE42 - 26819 - 245
18PROPROTHRTHRCC42 - 26819 - 245
28PROPROTHRTHRGG42 - 26819 - 245
19TYRTYRPHEPHEDD76 - 14134 - 99
29TYRTYRPHEPHEFF76 - 14134 - 99
110GLNGLNALAALADD73 - 14231 - 100
210GLNGLNALAALAHH73 - 14231 - 100
111PROPROTHRTHREE42 - 26819 - 245
211PROPROTHRTHRCC42 - 26819 - 245
112TYRTYRPHEPHEFF76 - 14134 - 99
212TYRTYRPHEPHEDD76 - 14134 - 99

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12

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Components

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


Mass: 27154.230 Da / Num. of mol.: 4 / Fragment: UNP residues 31-269
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LMAN1, ERGIC53, F5F8D / Plasmid: PCOLD-III / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CODONPLUS(DE3) / References: UniProt: P49257
#2: Protein
Multiple coagulation factor deficiency protein 2 / Neural stem cell-derived neuronal survival protein


Mass: 12056.186 Da / Num. of mol.: 4 / Fragment: UNP residues 67-146
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MCFD2, SDNSF / Plasmid: PET-16B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CODONPLUS(DE3) / References: UniProt: Q8NI22
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 238 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.55 Å3/Da / Density % sol: 51.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 17% PEG8000, 8% ethylene glycol, 0.1 M Tris-HCl

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jul 24, 2011
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 61522 / Num. obs: 61313 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 32.98 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 38.6
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.188 / Mean I/σ(I) obs: 9.8 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3A4U
Resolution: 2.4→20 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.906 / SU B: 7.094 / SU ML: 0.168 / Cross valid method: THROUGHOUT / ESU R: 0.339 / ESU R Free: 0.242 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.246 3081 5.1 %RANDOM
Rwork0.205 ---
obs0.207 57782 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.3 Å2
Baniso -1Baniso -2Baniso -3
1-2.09 Å20 Å21.98 Å2
2---3.48 Å20 Å2
3---0.15 Å2
Refinement stepCycle: 1 / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9087 0 20 238 9345
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0199317
X-RAY DIFFRACTIONr_bond_other_d0.0070.028455
X-RAY DIFFRACTIONr_angle_refined_deg1.5091.92212628
X-RAY DIFFRACTIONr_angle_other_deg1.2363.00119391
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.49851139
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.97924.8500
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.811151447
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9131544
X-RAY DIFFRACTIONr_chiral_restr0.0940.21312
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0210913
X-RAY DIFFRACTIONr_gen_planes_other0.0070.022335
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
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A133190.08
12C133190.08
21A131740.09
22E131740.09
31A132020.08
32C132020.08
41B32120.15
42D32120.15
51B26040.13
52F26040.13
61B27740.15
62D27740.15
71C132830.08
72E132830.08
81C133230.07
82G133230.07
91D27440.12
92F27440.12
101D28290.14
102H28290.14
111E133600.07
112C133600.07
121F26290.11
122D26290.11
LS refinement shellResolution: 2.4→2.46 Å
RfactorNum. reflection% reflection
Rfree0.317 203 -
Rwork0.261 4293 -
obs--99.8 %

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