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- PDB-3lcp: Crystal structure of the carbohydrate recognition domain of LMAN1... -

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Basic information

Entry
Database: PDB / ID: 3lcp
TitleCrystal structure of the carbohydrate recognition domain of LMAN1 in complex with MCFD2
Components
  • Multiple coagulation factor deficiency protein 2
  • Protein ERGIC-53
KeywordsPROTEIN BINDING / ER-GOLGI TRANSPORT / GLYCOPROTEIN SORTING / DISEASE MUTATION / SECRETORY PATHWAY / PROTEIN TRANSPORT / COAGULATION FACTOR DEFICIENCY / Disulfide bond / Endoplasmic reticulum / Golgi apparatus / Lectin / Membrane / Polymorphism / Transmembrane / Transport / Calcium
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: 2.45 Å
AuthorsWigren, E. / Bourhis, J.M. / Kursula, I. / Guy, J.E. / Lindqvist, Y.
CitationJournal: Febs Lett. / Year: 2010
Title: Crystal structure of the LMAN1-CRD/MCFD2 transport receptor complex provides insight into combined deficiency of factor V and factor VIII.
Authors: Wigren, E. / Bourhis, J.M. / Kursula, I. / Guy, J.E. / Lindqvist, Y.
History
DepositionJan 11, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 26, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)75,51212
Polymers75,1914
Non-polymers3218
Water1,964109
1
A: Protein ERGIC-53
C: Multiple coagulation factor deficiency protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7566
Polymers37,5962
Non-polymers1604
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2040 Å2
ΔGint-57 kcal/mol
Surface area14400 Å2
MethodPISA
2
B: Protein ERGIC-53
D: Multiple coagulation factor deficiency protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7566
Polymers37,5962
Non-polymers1604
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1990 Å2
ΔGint-45 kcal/mol
Surface area14530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.602, 58.602, 396.870
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22D
13E
23F
14G
24H

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A1 - 300
2111B1 - 300
1121C0 - 250
2121D0 - 250
1131E1 - 50
2131F1 - 50
1141G1 - 50
2141H1 - 50

NCS ensembles :
ID
1
2
3
4

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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: 27094.150 Da / Num. of mol.: 2
Fragment: UNP residues 32-277, Carbohydrate Recognition Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ERGIC53, F5F8D, LMAN1, LMAN1 (AMINO ACIDS 32-277) / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(de3) / References: UniProt: P49257
#2: Protein Multiple coagulation factor deficiency protein 2 / Neural stem cell-derived neuronal survival protein


Mass: 10501.501 Da / Num. of mol.: 2 / Fragment: UNP residues 58-146, 2 EF-hand domains
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MCFD2, MCFD2 (AMINO ACIDS 58-146), SDNSF / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(de3) / References: UniProt: Q8NI22
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 109 / 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: 2.62 Å3/Da / Density % sol: 52.99 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 205 PEG6000, 0.1 M Ammonium Chloride 0.1 M Hepes, pH 7., VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9537 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 10, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.732
11-H-K, K, -L20.268
ReflectionResolution: 2.45→50 Å / Num. obs: 28026 / % possible obs: 98.9 % / Observed criterion σ(I): 2 / Redundancy: 11.8 % / Rmerge(I) obs: 0.113 / Rsym value: 0.118 / Net I/σ(I): 17.6
Reflection shellResolution: 2.45→2.58 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 5.8 / Rsym value: 0.301

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Processing

Software
NameVersionClassification
DNAdata collection
PHASERphasing
REFMAC5.5.0102refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1R1Z

1r1z


Resolution: 2.45→50 Å / Cor.coef. Fo:Fc: 0.907 / Cor.coef. Fo:Fc free: 0.859 / SU B: 7.983 / SU ML: 0.19 / Cross valid method: THROUGHOUT / ESU R: 0.087 / ESU R Free: 0.056 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24726 1426 5.1 %RANDOM
Rwork0.19626 ---
obs0.19878 26465 98.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.544 Å2
Baniso -1Baniso -2Baniso -3
1-6.43 Å20 Å20 Å2
2--6.43 Å20 Å2
3----12.85 Å2
Refinement stepCycle: LAST / Resolution: 2.45→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4771 0 8 109 4888
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0224898
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4721.9336643
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5245599
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.09324.942259
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.87915766
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6441522
X-RAY DIFFRACTIONr_chiral_restr0.0930.2689
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213870
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.7941.52995
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.45824798
X-RAY DIFFRACTIONr_scbond_it2.18931903
X-RAY DIFFRACTIONr_scangle_it3.4844.51845
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1839TIGHT POSITIONAL0.120.05
1A1839TIGHT THERMAL0.130.5
2C542TIGHT POSITIONAL0.10.05
2C542TIGHT THERMAL0.120.5
3A18TIGHT POSITIONAL0.110.05
3A18TIGHT THERMAL0.220.5
4C4TIGHT POSITIONAL0.040.05
4C4TIGHT THERMAL0.190.5
LS refinement shellResolution: 2.45→2.511 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.405 87 -
Rwork0.261 1672 -
obs--85.6 %

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