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- PDB-4ygd: Crystal structure of ERGIC-53/MCFD2, monoclinic calcium-bound form 2 -

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Basic information

Entry
Database: PDB / ID: 4ygd
TitleCrystal structure of ERGIC-53/MCFD2, monoclinic calcium-bound form 2
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 / 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: 2.51 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
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)157,58927
Polymers156,8428
Non-polymers74819
Water5,278293
1
A: Protein ERGIC-53
B: Multiple coagulation factor deficiency protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,4428
Polymers39,2102
Non-polymers2316
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2280 Å2
ΔGint-82 kcal/mol
Surface area13740 Å2
MethodPISA
2
C: Protein ERGIC-53
D: Multiple coagulation factor deficiency protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,3716
Polymers39,2102
Non-polymers1604
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1800 Å2
ΔGint-57 kcal/mol
Surface area13340 Å2
MethodPISA
3
E: Protein ERGIC-53
F: Multiple coagulation factor deficiency protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,3716
Polymers39,2102
Non-polymers1604
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1750 Å2
ΔGint-57 kcal/mol
Surface area13510 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 area2140 Å2
ΔGint-72 kcal/mol
Surface area13790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.063, 58.765, 119.386
Angle α, β, γ (deg.)90.00, 109.01, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12A
22E
13A
23G
14B
24D
15B
25F
16B
26H
17C
27E
18C
28G
19D
29F
110D
210H
111E
211G
112F
212H

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROTHRTHRAA42 - 26819 - 245
21PROPROTHRTHRCC42 - 26819 - 245
12PROPROTHRTHRAA42 - 26819 - 245
22PROPROTHRTHREE42 - 26819 - 245
13PROPROTHRTHRAA42 - 26819 - 245
23PROPROTHRTHRGG42 - 26819 - 245
14PROPROALAALABB69 - 14227 - 100
24PROPROALAALADD69 - 14227 - 100
15METMETALAALABB67 - 14225 - 100
25METMETALAALAFF67 - 14225 - 100
16METMETLEULEUBB67 - 14525 - 103
26METMETLEULEUHH67 - 14525 - 103
17PROPROTHRTHRCC42 - 26819 - 245
27PROPROTHRTHREE42 - 26819 - 245
18PROPROTHRTHRCC42 - 26819 - 245
28PROPROTHRTHRGG42 - 26819 - 245
19PROPROPHEPHEDD69 - 14127 - 99
29PROPROPHEPHEFF69 - 14127 - 99
110PROPROLYSLYSDD69 - 14327 - 101
210PROPROLYSLYSHH69 - 14327 - 101
111PROPROTHRTHREE42 - 26819 - 245
211PROPROTHRTHRGG42 - 26819 - 245
112METMETALAALAFF67 - 14225 - 100
212METMETALAALAHH67 - 14225 - 100

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


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 293 / 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

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Sample preparation

CrystalDensity Matthews: 2.18 Å3/Da / Density % sol: 43.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 19% PEG3350, 8% ethylene glycol, 0.1 M Bis-Tris

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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: 2.5→50 Å / Num. all: 46552 / Num. obs: 46251 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 34.9
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.178 / Mean I/σ(I) obs: 8.8 / % possible all: 97.8

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3A4U

3a4u


Resolution: 2.51→20 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.936 / SU B: 8.294 / SU ML: 0.188 / Cross valid method: THROUGHOUT / ESU R: 0.649 / ESU R Free: 0.278 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.232 2318 5 %RANDOM
Rwork0.193 ---
obs0.195 43802 98.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.97 Å2
Baniso -1Baniso -2Baniso -3
1--1.41 Å20 Å20.8 Å2
2---1.67 Å20 Å2
3---2.26 Å2
Refinement stepCycle: 1 / Resolution: 2.51→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9252 0 19 293 9564
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0199488
X-RAY DIFFRACTIONr_bond_other_d0.0060.028625
X-RAY DIFFRACTIONr_angle_refined_deg1.5331.92312862
X-RAY DIFFRACTIONr_angle_other_deg1.143.00119789
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.10351160
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.76724.822506
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.134151476
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1951544
X-RAY DIFFRACTIONr_chiral_restr0.0990.21340
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211096
X-RAY DIFFRACTIONr_gen_planes_other0.0070.022368
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)
11A134970.04
12C134970.04
21A134640.04
22E134640.04
31A135510.02
32G135510.02
41B31290.15
42D31290.15
51B32110.15
52F32110.15
61B37590.06
62H37590.06
71C135530.03
72E135530.03
81C134770.04
82G134770.04
91D32530.09
92F32530.09
101D31750.16
102H31750.16
111E134720.04
112G134720.04
121F32020.15
122H32020.15
LS refinement shellResolution: 2.51→2.57 Å
RfactorNum. reflection% reflection
Rfree0.302 157 -
Rwork0.242 2948 -
obs--91.8 %

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