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- PDB-8jp5: Cryo-EM structures of the head region of full-length ERGIC-53 wit... -

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Basic information

Entry
Database: PDB / ID: 8jp5
TitleCryo-EM structures of the head region of full-length ERGIC-53 with MCFD2 (form B)
Components
  • Multiple coagulation factor deficiency protein 2
  • Protein ERGIC-53
KeywordsPROTEIN TRANSPORT / cargo receptor / calcium / zinc
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 / endoplasmic reticulum organization / RHOD GTPase cycle / 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 / endoplasmic reticulum organization / RHOD GTPase cycle / COPII-mediated vesicle transport / COPII-coated ER to Golgi transport vesicle / RHOC GTPase cycle / Golgi organization / D-mannose binding / endoplasmic reticulum-Golgi intermediate compartment / 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 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 domain pair / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain ...: / Legume-like lectin / : / Legume-like lectin family / L-type lectin-like (leguminous) domain profile. / 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
Similarity search - Domain/homology
Protein ERGIC-53 / Multiple coagulation factor deficiency protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.59 Å
AuthorsWatanabe, S. / Inaba, K.
Funding support Japan, 1items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology (Japan)JP18K06075 Japan
CitationJournal: Nat Commun / Year: 2024
Title: Structure of full-length ERGIC-53 in complex with MCFD2 for cargo transport.
Authors: Satoshi Watanabe / Yoshiaki Kise / Kento Yonezawa / Mariko Inoue / Nobutaka Shimizu / Osamu Nureki / Kenji Inaba /
Abstract: ERGIC-53 transports certain subsets of newly synthesized secretory proteins and membrane proteins from the endoplasmic reticulum to the Golgi apparatus. Despite numerous structural and functional ...ERGIC-53 transports certain subsets of newly synthesized secretory proteins and membrane proteins from the endoplasmic reticulum to the Golgi apparatus. Despite numerous structural and functional studies since its identification, the overall architecture and mechanism of action of ERGIC-53 remain unclear. Here we present cryo-EM structures of full-length ERGIC-53 in complex with its functional partner MCFD2. These structures reveal that ERGIC-53 exists as a homotetramer, not a homohexamer as previously suggested, and comprises a four-leaf clover-like head and a long stalk composed of three sets of four-helix coiled-coil followed by a transmembrane domain. 3D variability analysis visualizes the flexible motion of the long stalk and local plasticity of the head region. Notably, MCFD2 is shown to possess a Zn-binding site in its N-terminal lid, which appears to modulate cargo binding. Altogether, distinct mechanisms of cargo capture and release by ERGIC- 53 via the stalk bending and metal binding are proposed.
History
DepositionJun 10, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 17, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Data collection / Structure summary
Category: em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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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
E: Protein ERGIC-53
F: Protein ERGIC-53
G: Multiple coagulation factor deficiency protein 2
H: Multiple coagulation factor deficiency protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)291,77628
Polymers290,8738
Non-polymers90320
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "A" or chain "B" or chain "C" or chain "D"
d_2ens_1chain "E" or chain "F" or chain "G" or chain "H"

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11PROPROTHRTHRAA42 - 36742 - 367
d_12CACACACAAI601
d_13CACACACAAJ602
d_14PROPROSERSERBB42 - 36542 - 365
d_15CACACACABK601
d_16CACACACABL602
d_17METMETSERSERCC39 - 14417 - 122
d_18CACACACACM701
d_19CACACACACN702
d_110ZNZNZNZNCO703
d_111LEULEUSERSERDD41 - 14419 - 122
d_112CACACACADP701
d_113CACACACADQ702
d_21PROPROTHRTHREE42 - 36742 - 367
d_22CACACACAES601
d_23CACACACAET602
d_24PROPROSERSERFF42 - 36542 - 365
d_25CACACACAFU601
d_26CACACACAFV602
d_27METMETSERSERGG39 - 14417 - 122
d_28CACACACAGW701
d_29CACACACAGX702
d_210ZNZNZNZNGY703
d_211LEULEUSERSERHH41 - 14419 - 122
d_212CACACACAHZ701
d_213CACACACAHAA702

NCS oper: (Code: givenMatrix: (-0.99999982771, 0.000375640554633, 0.000451080187401), (-0.000375815230221, -0.999999854413, -0.000387216134887), (0.000450934667646, -0.000387385590978, 0.999999823295) ...NCS oper: (Code: given
Matrix: (-0.99999982771, 0.000375640554633, 0.000451080187401), (-0.000375815230221, -0.999999854413, -0.000387216134887), (0.000450934667646, -0.000387385590978, 0.999999823295)
Vector: 215.048513304, 215.201164656, -0.00934157152516)

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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: 58766.027 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LMAN1, ERGIC53, F5F8D / Production host: Homo sapiens (human) / References: UniProt: P49257
#2: Protein
Multiple coagulation factor deficiency protein 2 / Neural stem cell-derived neuronal survival protein


Mass: 13952.220 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MCFD2, SDNSF / Production host: Escherichia coli (E. coli) / References: UniProt: Q8NI22
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: ERGIC-53-MCFD2 complex / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1600 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 47.4 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
4cryoSPARC3CTF correction
7Cootmodel fitting
8UCSF ChimeraXmodel fitting
10cryoSPARC3.3initial Euler assignment
11cryoSPARC3.3final Euler assignment
14PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 2.59 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 81444 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 81.16 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002513784
ELECTRON MICROSCOPYf_angle_d0.577218618
ELECTRON MICROSCOPYf_chiral_restr0.04621916
ELECTRON MICROSCOPYf_plane_restr0.0042508
ELECTRON MICROSCOPYf_dihedral_angle_d17.35715136
Refine LS restraints NCSType: NCS constraints / Rms dev position: 0.000910743844502 Å

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