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- PDB-5w1m: MACV GP1 CR1-07 Fab complex -

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Basic information

Entry
Database: PDB / ID: 5w1m
TitleMACV GP1 CR1-07 Fab complex
Components
  • CR1-07 Fab heavy chain
  • CR1-07 Fab light chain
  • Pre-glycoprotein polyprotein GP complex
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / Fab / antibody / Machupo virus / arenavirus / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


host cell Golgi membrane / immunoglobulin complex, circulating / immunoglobulin receptor binding / complement activation, classical pathway / antigen binding / antibacterial humoral response / receptor-mediated endocytosis of virus by host cell / host cell endoplasmic reticulum membrane / blood microparticle / immune response ...host cell Golgi membrane / immunoglobulin complex, circulating / immunoglobulin receptor binding / complement activation, classical pathway / antigen binding / antibacterial humoral response / receptor-mediated endocytosis of virus by host cell / host cell endoplasmic reticulum membrane / blood microparticle / immune response / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / extracellular space / extracellular exosome / membrane / metal ion binding / plasma membrane
Similarity search - Function
Arenavirus glycoprotein, zinc binding domain / Arenavirus glycoprotein / Arenavirus glycoprotein / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. ...Arenavirus glycoprotein, zinc binding domain / Arenavirus glycoprotein / Arenavirus glycoprotein / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
beta-D-mannopyranose / Immunoblobulin light chain / Ig-like domain-containing protein / Pre-glycoprotein polyprotein GP complex
Similarity search - Component
Biological speciesHomo sapiens (human)
Machupo virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.91 Å
AuthorsRaymond, D.D. / Clark, L.E. / Abraham, J.
Funding support United States, 5items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI007061 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI109740 United States
Other privateBurroughs Wellcome United States
Other privateWilliam Randolph Hearst Foundation and Brigham and Womens Hospital United States
Other privateHarvard Medical School DICP United States
CitationJournal: Nat Commun / Year: 2018
Title: Vaccine-elicited receptor-binding site antibodies neutralize two New World hemorrhagic fever arenaviruses.
Authors: Clark, L.E. / Mahmutovic, S. / Raymond, D.D. / Dilanyan, T. / Koma, T. / Manning, J.T. / Shankar, S. / Levis, S.C. / Briggiler, A.M. / Enria, D.A. / Wucherpfennig, K.W. / Paessler, S. / Abraham, J.
History
DepositionJun 3, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 30, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_seq_id_1 / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CR1-07 Fab light chain
B: CR1-07 Fab heavy chain
C: CR1-07 Fab light chain
D: CR1-07 Fab heavy chain
E: CR1-07 Fab light chain
F: CR1-07 Fab heavy chain
G: CR1-07 Fab light chain
H: CR1-07 Fab heavy chain
Q: Pre-glycoprotein polyprotein GP complex
R: Pre-glycoprotein polyprotein GP complex
S: Pre-glycoprotein polyprotein GP complex
T: Pre-glycoprotein polyprotein GP complex
hetero molecules


Theoretical massNumber of molelcules
Total (without water)265,98117
Polymers264,14412
Non-polymers1,8375
Water00
1
A: CR1-07 Fab light chain
B: CR1-07 Fab heavy chain
R: Pre-glycoprotein polyprotein GP complex
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,4604
Polymers66,0363
Non-polymers4241
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: CR1-07 Fab light chain
D: CR1-07 Fab heavy chain
T: Pre-glycoprotein polyprotein GP complex
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,2574
Polymers66,0363
Non-polymers2211
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: CR1-07 Fab light chain
F: CR1-07 Fab heavy chain
Q: Pre-glycoprotein polyprotein GP complex
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,6415
Polymers66,0363
Non-polymers6052
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: CR1-07 Fab light chain
H: CR1-07 Fab heavy chain
S: Pre-glycoprotein polyprotein GP complex
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,6234
Polymers66,0363
Non-polymers5871
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)206.970, 206.970, 238.230
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212

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Components

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Protein , 1 types, 4 molecules QRST

#3: Protein
Pre-glycoprotein polyprotein GP complex / MACV GP1


Mass: 17454.875 Da / Num. of mol.: 4 / Fragment: UNP residues 87-238
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Machupo virus / Gene: GPC / Production host: Homo sapiens (human) / References: UniProt: Q8AZ57

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Antibody , 2 types, 8 molecules ACEGBDFH

#1: Antibody
CR1-07 Fab light chain


Mass: 24289.822 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) / References: UniProt: Q0KKI6
#2: Antibody
CR1-07 Fab heavy chain


Mass: 24291.330 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) / References: UniProt: Q6N089

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Sugars , 4 types, 5 molecules

#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#5: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#6: Sugar ChemComp-BMA / beta-D-mannopyranose / beta-D-mannose / D-mannose / mannose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DManpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-mannopyranoseCOMMON NAMEGMML 1.0
b-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0
#7: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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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: 4.87 Å3/Da / Density % sol: 74.74 %
Crystal growTemperature: 297 K / Method: batch mode / pH: 5.5 / Details: 1.8 M AmSO4 and 100 mM NaCitrate pH 5.5.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 12, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.91→49.12 Å / Num. obs: 46832 / % possible obs: 98.8 % / Redundancy: 8.073 % / Biso Wilson estimate: 145.49 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.329 / Rrim(I) all: 0.351 / Χ2: 1.02 / Net I/σ(I): 7.72 / Num. measured all: 378092 / Scaling rejects: 193
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
3.91-4.158.1168.380.5259863762173760.2158.9496.8
4.15-4.438.2492.6251.2557007693769110.4952.79799.6
4.43-4.788.2381.5322.1553993658165540.7511.63399.6
4.78-5.248.1980.8713.4950412617361490.8810.92999.6
5.24-5.848.1660.6524.4244300546454250.9220.69699.3
5.84-6.738.0950.4276.3139740494349090.9570.45699.3
6.73-8.217.9470.17212.9233344423741960.9930.18499
8.21-11.457.5430.04733.424884334132990.9990.0598.7
11.45-49.127.2280.02946.8914549209320130.9990.03196.2

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XSCALEdata scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2WFO

2wfo


Resolution: 3.91→49.12 Å / Cor.coef. Fo:Fc: 0.424 / Cor.coef. Fo:Fc free: 0.41 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.636
RfactorNum. reflection% reflectionSelection details
Rfree0.264 2332 5 %RANDOM
Rwork0.248 ---
obs0.249 46614 98.6 %-
Displacement parametersBiso max: 108.13 Å2 / Biso mean: 33.45 Å2 / Biso min: 11.07 Å2
Baniso -1Baniso -2Baniso -3
1--28.4685 Å20 Å20 Å2
2---28.4685 Å20 Å2
3---56.937 Å2
Refine analyzeLuzzati coordinate error obs: 0.81 Å
Refinement stepCycle: final / Resolution: 3.91→49.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18299 0 120 0 18419
Biso mean--30 --
Num. residues----2360
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d6391SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes3163HARMONIC5
X-RAY DIFFRACTIONt_it18911HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion2438SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact20068SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d18911HARMONIC20.012
X-RAY DIFFRACTIONt_angle_deg25686HARMONIC21.33
X-RAY DIFFRACTIONt_omega_torsion2.88
X-RAY DIFFRACTIONt_other_torsion21.05
LS refinement shellResolution: 3.91→4.01 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2602 153 5.03 %
Rwork0.2586 2888 -
all0.2586 3041 -
obs--88.97 %

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