[English] 日本語
Yorodumi
- PDB-4rfo: Crystal structure of the ADCC-Potent Antibody N60-I3 Fab in compl... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4rfo
TitleCrystal structure of the ADCC-Potent Antibody N60-I3 Fab in complex with HIV-1 Clade A/E gp120 and M48u1
Components
  • HIV-1 clade A/E gp120
  • N60-i3 Fab heavy chain
  • N60-i3 Fab light chain
  • m48u1 CD4 mimetic peptide
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM/INHIBITOR / HIV-1 GP120 / CLADE A/E 93TH057 / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM-INHIBITOR complex
Function / homology
Function and homology information


positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope ...positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / apoptotic process / host cell plasma membrane / structural molecule activity / virion membrane / plasma membrane
Similarity search - Function
HIV Envelope Protein Gp120; Chain G / Human immunodeficiency virus 1, Gp160, envelope glycoprotein / Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Beta Complex / Immunoglobulins ...HIV Envelope Protein Gp120; Chain G / Human immunodeficiency virus 1, Gp160, envelope glycoprotein / Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Beta Complex / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
CD4-MIMETIC MINIPROTEIN M48U1 / Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
Homo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsTolbert, W.D. / Gohain, N. / Pazgier, M.
CitationJournal: J.Virol. / Year: 2015
Title: Cocrystal Structures of Antibody N60-i3 and Antibody JR4 in Complex with gp120 Define More Cluster A Epitopes Involved in Effective Antibody-Dependent Effector Function against HIV-1.
Authors: Gohain, N. / Tolbert, W.D. / Acharya, P. / Yu, L. / Liu, T. / Zhao, P. / Orlandi, C. / Visciano, M.L. / Kamin-Lewis, R. / Sajadi, M.M. / Martin, L. / Robinson, J.E. / Kwong, P.D. / DeVico, A. ...Authors: Gohain, N. / Tolbert, W.D. / Acharya, P. / Yu, L. / Liu, T. / Zhao, P. / Orlandi, C. / Visciano, M.L. / Kamin-Lewis, R. / Sajadi, M.M. / Martin, L. / Robinson, J.E. / Kwong, P.D. / DeVico, A.L. / Ray, K. / Lewis, G.K. / Pazgier, M.
History
DepositionSep 26, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 19, 2015Group: Database references
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.pdbx_value_order / _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_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Jun 2, 2021Group: Source and taxonomy / Structure summary / Category: chem_comp / entity_src_gen
Item: _chem_comp.pdbx_synonyms / _entity_src_gen.host_org_common_name ..._chem_comp.pdbx_synonyms / _entity_src_gen.host_org_common_name / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.4Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Dec 6, 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: HIV-1 clade A/E gp120
N: m48u1 CD4 mimetic peptide
H: N60-i3 Fab heavy chain
L: N60-i3 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,96313
Polymers89,9724
Non-polymers1,9919
Water181
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)98.305, 102.575, 108.038
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

-
Antibody , 2 types, 2 molecules HL

#3: Antibody N60-i3 Fab heavy chain


Mass: 24412.373 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: FAB HEAVY CHAIN OF ADCC-POTENT ANTI-HIV-1 ANTIBODY N60-i3
Cell line (production host): HEK 293 / Production host: Homo sapiens (human)
#4: Antibody N60-i3 Fab light chain


Mass: 23342.707 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: FAB LIGHT CHAIN OF ADCC-POTENT ANTI-HIV-1 ANTIBODY N60-i3
Cell line (production host): HEK 293 / Production host: Homo sapiens (human)

-
Protein / Protein/peptide / Sugars / Non-polymers , 4 types, 12 molecules GN

#1: Protein HIV-1 clade A/E gp120


Mass: 39160.367 Da / Num. of mol.: 1 / Mutation: H375S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: HIV-1 env / Cell line (production host): HEK 293 GnT1- / Production host: Homo sapiens (human) / References: UniProt: Q0ED31*PLUS
#2: Protein/peptide m48u1 CD4 mimetic peptide


Type: Peptide-like / Class: Inhibitor / Mass: 3056.804 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: M48U1 is an engineered CD4 mimetic / Source: (synth.) synthetic construct (others) / References: CD4-MIMETIC MINIPROTEIN M48U1
#5: 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.: 9
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
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O

-
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

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.03 Å3/Da / Density % sol: 59.37 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 10-16% PEG 8000, 0.1 M Tris-HCl pH 8.5, 65 mM NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 294K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.12709 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 31, 2013 / Details: RH coated flat mirror
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12709 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. all: 18694 / Num. obs: 17516 / % possible obs: 93.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rmerge(I) obs: 0.126 / Net I/σ(I): 10.7
Reflection shellResolution: 3.2→3.26 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.899 / Mean I/σ(I) obs: 1.3 / % possible all: 96

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.8.0073/Phenix 1.9refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3TNN FOR N60-I3, PDB ENTRY 4H8W FOR GP120, PDB ENTRY 4JZW FOR M48U1

3tnn

4h8w

4jzw


Resolution: 3.2→36.013 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.892 / SU B: 73.662 / SU ML: 0.543 / Cross valid method: THROUGHOUT / ESU R Free: 0.562 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27702 876 5 %RANDOM
Rwork0.21981 ---
obs0.2226 16589 93.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 116.914 Å2
Baniso -1Baniso -2Baniso -3
1-0.98 Å20 Å2-0 Å2
2---8.03 Å2-0 Å2
3---7.05 Å2
Refinement stepCycle: LAST / Resolution: 3.2→36.013 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6042 0 126 1 6169
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.026328
X-RAY DIFFRACTIONr_bond_other_d0.0020.025859
X-RAY DIFFRACTIONr_angle_refined_deg1.4111.9698547
X-RAY DIFFRACTIONr_angle_other_deg0.836313494
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8345762
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.93625.143245
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.34151005
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.5571518
X-RAY DIFFRACTIONr_chiral_restr0.080.2994
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0216899
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021361
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_it1.8136.3943147
X-RAY DIFFRACTIONr_mcbond_other1.8136.3943146
X-RAY DIFFRACTIONr_mcangle_it3.1019.6013863
X-RAY DIFFRACTIONr_mcangle_other3.0729.5153912
X-RAY DIFFRACTIONr_scbond_it2.2266.6243181
X-RAY DIFFRACTIONr_scbond_other1.9716.5763190
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.3049.8194716
X-RAY DIFFRACTIONr_long_range_B_refined7.91660.47625361
X-RAY DIFFRACTIONr_long_range_B_other7.91660.47925362
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.2→3.283 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 65 -
Rwork0.35 1214 -
obs--95.38 %
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)
13.31470.33020.14064.64681.59854.89510.1678-0.36990.44810.6416-0.29610.4217-0.3286-0.41490.12820.2384-0.04130.11910.236-0.00740.156112.7138113.3152112.9531
25.45596.46124.15987.87534.74133.32890.2419-0.198-0.5120.3036-0.1058-0.89810.165-0.2308-0.13610.4404-0.06760.01270.213-0.10990.453626.1465130.5376116.8838
31.8028-1.0647-2.50412.64112.62985.2389-0.31560.5931-0.5191-0.28460.02280.11630.6361-0.00040.29290.39930.0084-0.0310.7158-0.32340.287722.767289.735266.1348
40.9053-0.941-1.69732.8392.82655.35370.34650.52910.0039-1.2192-0.0888-0.5278-1.06680.339-0.25770.8009-0.01330.09831.1627-0.0640.229532.6221103.073758.8227
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1G44 - 492
2X-RAY DIFFRACTION2N2 - 27
3X-RAY DIFFRACTION3H1 - 212
4X-RAY DIFFRACTION4L1 - 208

+
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