[English] 日本語
Yorodumi
- PDB-6mfp: Crystal Structure of the RV305 C1-C2 specific ADCC potent antibod... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6mfp
TitleCrystal Structure of the RV305 C1-C2 specific ADCC potent antibody DH677.3 Fab in complex with HIV-1 clade A/E gp120 and M48U1
Components
  • DH677.3 Fab heavy chain
  • DH677.3 Fab light chain
  • M48U1 CD4 MIMETIC PEPTIDE
  • clade A/E 93TH057 HIV-1 gp120 core
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / ANTI-HIV-1 ENV ANTIBODY DH677.3 / CD4I ANTIBODY / ADCC / HIV-1 ENV / IMMUNE SYSTEM / RV305 VACCINE TRIAL / HIV-1 GP120 / CLADE A/E 93TH057 / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


membrane fusion involved in viral entry into host cell / viral envelope / symbiont entry into host cell / virion attachment to host cell / virion membrane
Similarity search - Function
Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
CD4-MIMETIC MINIPROTEIN M48U1 / clade A/E 93TH057 HIV-1 gp120 core
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
Homo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsTolbert, W.D. / Young, B. / Pazgier, M.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI16274 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P01AI120756 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI129769 United States
CitationJournal: J.Virol. / Year: 2020
Title: Boosting with AIDSVAX B/E Enhances Env Constant Region 1 and 2 Antibody-Dependent Cellular Cytotoxicity Breadth and Potency.
Authors: Easterhoff, D. / Pollara, J. / Luo, K. / Tolbert, W.D. / Young, B. / Mielke, D. / Jha, S. / O'Connell, R.J. / Vasan, S. / Kim, J. / Michael, N.L. / Excler, J.L. / Robb, M.L. / Rerks-Ngarm, S. ...Authors: Easterhoff, D. / Pollara, J. / Luo, K. / Tolbert, W.D. / Young, B. / Mielke, D. / Jha, S. / O'Connell, R.J. / Vasan, S. / Kim, J. / Michael, N.L. / Excler, J.L. / Robb, M.L. / Rerks-Ngarm, S. / Kaewkungwal, J. / Pitisuttithum, P. / Nitayaphan, S. / Sinangil, F. / Tartaglia, J. / Phogat, S. / Kepler, T.B. / Alam, S.M. / Wiehe, K. / Saunders, K.O. / Montefiori, D.C. / Tomaras, G.D. / Moody, M.A. / Pazgier, M. / Haynes, B.F. / Ferrari, G.
History
DepositionSep 11, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2019Group: Data collection / Derived calculations / Category: pdbx_struct_assembly_gen / Item: _pdbx_struct_assembly_gen.asym_id_list
Revision 1.2Nov 6, 2019Group: Data collection / Structure summary / Category: pdbx_entry_details / pdbx_molecule_features / Item: _pdbx_entry_details.compound_details
Revision 1.3Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Apr 1, 2020Group: Data collection / Database references / Category: chem_comp / citation / citation_author
Item: _chem_comp.type / _citation.country ..._chem_comp.type / _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
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_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _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 / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _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 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 2.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
G: clade A/E 93TH057 HIV-1 gp120 core
N: M48U1 CD4 MIMETIC PEPTIDE
H: DH677.3 Fab heavy chain
L: DH677.3 Fab light chain
A: clade A/E 93TH057 HIV-1 gp120 core
M: M48U1 CD4 MIMETIC PEPTIDE
C: DH677.3 Fab heavy chain
D: DH677.3 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)186,09734
Polymers180,3678
Non-polymers5,72926
Water00
1
G: clade A/E 93TH057 HIV-1 gp120 core
N: M48U1 CD4 MIMETIC PEPTIDE
H: DH677.3 Fab heavy chain
L: DH677.3 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,83816
Polymers90,1844
Non-polymers2,65412
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: clade A/E 93TH057 HIV-1 gp120 core
M: M48U1 CD4 MIMETIC PEPTIDE
C: DH677.3 Fab heavy chain
D: DH677.3 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,25818
Polymers90,1844
Non-polymers3,07514
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.487, 80.093, 88.688
Angle α, β, γ (deg.)84.82, 82.33, 82.24
Int Tables number1
Space group name H-MP1

-
Components

-
Antibody , 2 types, 4 molecules HCLD

#3: Antibody DH677.3 Fab heavy chain


Mass: 24504.537 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell (production host): HEK 293 / Production host: Homo sapiens (human)
#4: Antibody DH677.3 Fab light chain


Mass: 23265.709 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell (production host): HEK 293 / Production host: Homo sapiens (human)

-
Protein / Protein/peptide / Non-polymers , 3 types, 6 molecules GANM

#1: Protein clade A/E 93TH057 HIV-1 gp120 core


Mass: 39356.613 Da / Num. of mol.: 2 / Mutation: H375S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: HIV-1 Env / Cell (production host): HEK 293 GnT1- cells / Production host: Homo sapiens (human) / References: UniProt: A0A0M3KKW9
#2: Protein/peptide M48U1 CD4 MIMETIC PEPTIDE


Type: Peptide-like / Class: Inhibitor / Mass: 3056.804 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: CD4-MIMETIC MINIPROTEIN M48U1
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl

-
Sugars , 2 types, 24 molecules

#5: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#6: 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.: 23 / Source method: obtained synthetically / 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

-
Details

Compound detailsTHE CD4-MIMETIC MINIPROTEINS INHIBIT HIV-1 ENTRY AND ARE DERIVED FROM SCYLLATOXIN (A SCORPION TOXIN) ...THE CD4-MIMETIC MINIPROTEINS INHIBIT HIV-1 ENTRY AND ARE DERIVED FROM SCYLLATOXIN (A SCORPION TOXIN) BY TRANSPLANTING THE GP120-INTERACTIVE REGION OF CD4 ONTO THE SCYLLATOXIN SCAFFOLD, FOLLOWED BY MANY ROUNDS OF ITERATIVE OPTIMIZATION
Sequence detailsAuthors state that Val 42 and Pro 43 of HIV-1 gp120 core are missing from UNP A0A0M3KKW9 but are ...Authors state that Val 42 and Pro 43 of HIV-1 gp120 core are missing from UNP A0A0M3KKW9 but are part of the protein and not an expression tag

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.45 Å3/Da / Density % sol: 49.77 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 25% PEG 4000 0.1 M MES pH 5.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 25, 2018
RadiationMonochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 30469 / % possible obs: 89.1 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 10.2
Reflection shellResolution: 3→3.05 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.442 / Num. unique obs: 1547 / % possible all: 90.7

-
Processing

Software
NameVersionClassification
REFMAC5.8.0232refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TGT, 6MFJ

3tgt

6mfj


Resolution: 3→39.6 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.905 / SU B: 79.988 / SU ML: 0.629 / Cross valid method: THROUGHOUT / ESU R Free: 0.576 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.274 1492 4.9 %RANDOM
Rwork0.214 ---
obs0.217 28977 88.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 93.95 Å2
Baniso -1Baniso -2Baniso -3
1-1.84 Å21.48 Å2-3.11 Å2
2---0.25 Å2-1.24 Å2
3----2.01 Å2
Refinement stepCycle: LAST / Resolution: 3→39.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12342 0 362 0 12704
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01313024
X-RAY DIFFRACTIONr_bond_other_d0.0010.01711668
X-RAY DIFFRACTIONr_angle_refined_deg1.4511.69217715
X-RAY DIFFRACTIONr_angle_other_deg1.1841.61427279
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.98151577
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.97723.833574
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.934152080
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0441546
X-RAY DIFFRACTIONr_chiral_restr0.0530.21812
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214257
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022521
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_it2.5286.5666388
X-RAY DIFFRACTIONr_mcbond_other2.5286.5666387
X-RAY DIFFRACTIONr_mcangle_it4.1619.8227931
X-RAY DIFFRACTIONr_mcangle_other4.1619.8237932
X-RAY DIFFRACTIONr_scbond_it2.6886.976636
X-RAY DIFFRACTIONr_scbond_other2.6896.9696634
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.50910.369784
X-RAY DIFFRACTIONr_long_range_B_refined9.89150216
X-RAY DIFFRACTIONr_long_range_B_other9.89250212
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3→3.08 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 104 -
Rwork0.327 2144 -
obs--87.81 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.1975-0.18542.36812.4258-0.64623.84360.1617-0.25480.1638-0.2282-0.06440.18570.4135-0.6992-0.09730.1549-0.1358-0.07820.24090.05540.0567-4.7413-17.54032.5485
22.4809-0.79462.64321.2924-1.26583.4719-0.4122-0.91730.4910.50080.0958-0.2198-0.3968-0.68830.31640.30080.1028-0.19930.6108-0.23550.385425.1021-16.542849.7816
32.5873-0.95522.50831.1261-1.71274.78790.0087-0.33670.42440.0988-0.2586-0.43040.43590.14450.24990.2068-0.0361-0.17370.2490.04580.298838.1944-28.563545.0329
44.75140.2182-0.12331.54390.18944.10660.084-0.9275-0.23210.1586-0.0935-0.0332-0.20640.2520.00950.1335-0.1405-0.11460.30420.15640.123521.325820.168660.2263
55.4391-1.02522.38142.7492-0.97942.18660.38860.389-0.5621-0.7659-0.08640.75020.4609-0.134-0.30220.3883-0.0143-0.33090.1191-0.06480.3327-18.350611.584421.7658
63.9588-0.03891.75372.111-0.17012.2975-0.12980.24780.3256-0.42030.0830.74540.11-0.17440.04680.2343-0.0525-0.25420.07020.06010.3544-23.461329.259219.5054
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1G44 - 492
2X-RAY DIFFRACTION2H1 - 214
3X-RAY DIFFRACTION3L1 - 213
4X-RAY DIFFRACTION4A44 - 492
5X-RAY DIFFRACTION5C1 - 214
6X-RAY DIFFRACTION6D1 - 213

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more