[English] 日本語
Yorodumi
- PDB-4xmp: Crystal structure of broadly and potently neutralizing antibody V... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4xmp
TitleCrystal structure of broadly and potently neutralizing antibody VRC08 in complex with HIV-1 clade A strain Q842.d12 gp120
Components
  • Envelope glycoprotein gp160,Envelope glycoprotein gp160,Envelope glycoprotein gp160
  • HEAVY CHAIN OF ANTIBODY VRC08
  • LIGHT CHAIN OF ANTIBODY VRC08
KeywordsIMMUNE SYSTEM / Antibody / HIV-1
Function / homology
Function and homology information


IgD immunoglobulin complex / IgM immunoglobulin complex / IgA immunoglobulin complex / IgE immunoglobulin complex / CD22 mediated BCR regulation / complement-dependent cytotoxicity / antibody-dependent cellular cytotoxicity / Fc epsilon receptor (FCERI) signaling / Fc-gamma receptor I complex binding / Classical antibody-mediated complement activation ...IgD immunoglobulin complex / IgM immunoglobulin complex / IgA immunoglobulin complex / IgE immunoglobulin complex / CD22 mediated BCR regulation / complement-dependent cytotoxicity / antibody-dependent cellular cytotoxicity / Fc epsilon receptor (FCERI) signaling / Fc-gamma receptor I complex binding / Classical antibody-mediated complement activation / Initial triggering of complement / immunoglobulin complex, circulating / IgG immunoglobulin complex / immunoglobulin receptor binding / immunoglobulin mediated immune response / FCGR activation / Role of phospholipids in phagocytosis / Role of LAT2/NTAL/LAB on calcium mobilization / Scavenging of heme from plasma / complement activation, classical pathway / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / antigen binding / positive regulation of establishment of T cell polarity / virus-mediated perturbation of host defense response / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / host cell endosome membrane / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / Regulation of Complement cascade / Cell surface interactions at the vascular wall / FCGR3A-mediated phagocytosis / FCERI mediated MAPK activation / B cell receptor signaling pathway / Regulation of actin dynamics for phagocytic cup formation / FCERI mediated NF-kB activation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / antibacterial humoral response / clathrin-dependent endocytosis of virus by host cell / blood microparticle / Interleukin-4 and Interleukin-13 signaling / Potential therapeutics for SARS / adaptive immune response / viral protein processing / immune response / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / extracellular space / extracellular exosome / extracellular region / 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 / Immunoglobulin/major histocompatibility complex, conserved site ...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 / 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
(R,R)-2,3-BUTANEDIOL / Immunoglobulin kappa constant / Immunoglobulin heavy constant gamma 1 / Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7831 Å
AuthorsZhou, T. / Srivatsan, S. / Kwong, P.D.
CitationJournal: Cell / Year: 2015
Title: Maturation and Diversity of the VRC01-Antibody Lineage over 15 Years of Chronic HIV-1 Infection.
Authors: Wu, X. / Zhang, Z. / Schramm, C.A. / Joyce, M.G. / Do Kwon, Y. / Zhou, T. / Sheng, Z. / Zhang, B. / O'Dell, S. / McKee, K. / Georgiev, I.S. / Chuang, G.Y. / Longo, N.S. / Lynch, R.M. / ...Authors: Wu, X. / Zhang, Z. / Schramm, C.A. / Joyce, M.G. / Do Kwon, Y. / Zhou, T. / Sheng, Z. / Zhang, B. / O'Dell, S. / McKee, K. / Georgiev, I.S. / Chuang, G.Y. / Longo, N.S. / Lynch, R.M. / Saunders, K.O. / Soto, C. / Srivatsan, S. / Yang, Y. / Bailer, R.T. / Louder, M.K. / Mullikin, J.C. / Connors, M. / Kwong, P.D. / Mascola, J.R. / Shapiro, L.
History
DepositionJan 15, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 29, 2015Provider: repository / Type: Initial release
Revision 1.1May 6, 2015Group: Database references
Revision 2.0Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Polymer sequence / Source and taxonomy / Structure summary
Category: chem_comp / entity ...chem_comp / entity / entity_poly / entity_src_gen / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_oper_list / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.pdbx_alt_source_flag / _pdbx_entity_nonpoly.name / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 27, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
G: Envelope glycoprotein gp160,Envelope glycoprotein gp160,Envelope glycoprotein gp160
H: HEAVY CHAIN OF ANTIBODY VRC08
L: LIGHT CHAIN OF ANTIBODY VRC08
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,55016
Polymers87,9363
Non-polymers2,61413
Water11,313628
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.713, 82.496, 163.066
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

-
Antibody , 2 types, 2 molecules HL

#2: Antibody HEAVY CHAIN OF ANTIBODY VRC08


Mass: 25258.582 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pVRC8400 / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: P01857*PLUS
#3: Antibody LIGHT CHAIN OF ANTIBODY VRC08


Mass: 23009.785 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pVRC8400 / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: P01834*PLUS

-
Protein / Sugars , 2 types, 12 molecules G

#1: Protein Envelope glycoprotein gp160,Envelope glycoprotein gp160,Envelope glycoprotein gp160


Mass: 39667.828 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 43-122, 195-297, 319-481
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Strain: Q842.d12 / Gene: env / Plasmid: pVRC8400 / Cell line (production host): HEK 293 GNTI- / Production host: Homo sapiens (human) / References: UniProt: Q8JDI3
#4: 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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 11 / 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

-
Non-polymers , 2 types, 630 molecules

#5: Chemical ChemComp-BU3 / (R,R)-2,3-BUTANEDIOL


Mass: 90.121 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 628 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.66 Å3/Da / Density % sol: 53.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 13% PEG 1500, 2% MPD, 0.1M Tris-HCl, pH 8.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 4, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.78→50 Å / Num. obs: 88301 / % possible obs: 97.9 % / Redundancy: 6 % / Biso Wilson estimate: 25.55 Å2 / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.043 / Rrim(I) all: 0.105 / Χ2: 1.37 / Net I/av σ(I): 20.167 / Net I/σ(I): 10.3 / Num. measured all: 528269
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.78-1.814.20.6022.3239740.7880.3110.6811.08889.9
1.81-1.844.60.55941690.8230.2790.6271.06693.3
1.84-1.884.90.51442990.8810.2480.5731.11596
1.88-1.925.30.48643390.8930.2280.5381.1597.7
1.92-1.965.60.4143870.9240.1870.4521.25698.3
1.96-25.90.35843600.950.1590.3931.25698
2-2.056.20.31743990.9620.1380.3471.32198.1
2.05-2.116.40.28543940.970.1220.311.35298.3
2.11-2.176.50.26244040.9760.1110.2851.4398.8
2.17-2.246.60.23444180.9810.0980.2541.57398.6
2.24-2.326.70.20844220.9830.0870.2261.51398.7
2.32-2.426.70.17744690.9870.0740.1931.55299
2.42-2.536.70.14944270.990.0630.1631.55499.2
2.53-2.666.70.12844770.9910.0540.1391.41399.2
2.66-2.836.60.10344840.9940.0440.1121.41199.1
2.83-3.046.50.09145010.9930.0390.0991.48599.2
3.04-3.356.30.07445080.9950.0320.0811.4699.4
3.35-3.836.20.06945520.9950.030.0751.26599.5
3.83-4.835.80.07345870.9930.0330.081.29999.1
4.83-5050.07547310.9910.0380.0841.40397.8

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
PHENIXdev_1702refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3SE9,4J6R

3se9

4j6r


Resolution: 1.7831→35.499 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2012 4409 5 %
Rwork0.1646 83719 -
obs0.1664 88128 97.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 345.73 Å2 / Biso mean: 49.8852 Å2 / Biso min: 15.21 Å2
Refinement stepCycle: final / Resolution: 1.7831→35.499 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6037 0 329 628 6994
Biso mean--79.29 44.68 -
Num. residues----780
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086371
X-RAY DIFFRACTIONf_angle_d1.0858655
X-RAY DIFFRACTIONf_chiral_restr0.0451005
X-RAY DIFFRACTIONf_plane_restr0.0051106
X-RAY DIFFRACTIONf_dihedral_angle_d12.4122292
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7831-1.80340.30331190.26442280239981
1.8034-1.82460.30051590.25892523268290
1.8246-1.84680.33781400.25152643278394
1.8468-1.87020.27971410.24262687282895
1.8702-1.89480.26021540.22942727288197
1.8948-1.92080.26731520.23042748290097
1.9208-1.94820.22381470.20862785293298
1.9482-1.97730.22921410.20252762290398
1.9773-2.00820.23771310.19782791292298
2.0082-2.04110.23221440.1952805294998
2.0411-2.07630.24151400.19482795293599
2.0763-2.1140.21181460.1792787293398
2.114-2.15470.21921570.179527982955100
2.1547-2.19870.21371540.18182778293298
2.1987-2.24650.21291230.17212836295998
2.2465-2.29870.20611290.177428682997100
2.2987-2.35620.22911590.17022776293599
2.3562-2.41990.20471680.17592795296399
2.4199-2.49110.22771670.1742790295799
2.4911-2.57150.21661400.179228663006100
2.5715-2.66330.21031570.17492806296399
2.6633-2.76990.21961670.17292851301899
2.7699-2.89590.21141520.17522813296599
2.8959-3.04850.1951510.17262848299999
3.0485-3.23940.22161370.16912862299999
3.2394-3.48930.20651590.15812883304299
3.4893-3.84010.18021460.147728993045100
3.8401-4.39490.16581530.126629003053100
4.3949-5.53370.14811300.11622964309499
5.5337-35.50650.16011460.15533053319998
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)
15.78693.36143.6828.76765.15633.6664-0.12160.1407-0.3423-0.3226-0.0740.3325-0.0523-0.47410.19150.27260.04880.03470.4286-0.07250.247957.293394.5724166.1867
23.39411.36510.9064.28761.82443.29610.0626-0.1921-0.14060.0392-0.16930.24520.1785-0.50780.06820.17680.02540.02410.3305-0.0020.161962.870988.7831161.2851
31.67760.27210.25211.94780.38932.764-0.0024-0.2454-0.1110.1693-0.0292-0.06030.18730.11260.00220.16840.03650.00960.19390.02250.155383.908986.8889163.2896
41.94141.31771.00878.60680.21016.4779-0.0483-0.1236-0.2984-0.20730.0210.33720.3162-0.45370.10190.1930.01150.05020.2252-0.04050.15961.845683.5817156.4981
53.69250.6649-1.54271.3356-0.08772.5539-0.07010.0224-0.0209-0.03180.0319-0.0101-0.11970.01280.05210.17140.0182-0.0220.1126-0.02880.122988.933994.9776137.8069
63.90170.91730.85883.6029-0.16654.7394-0.18390.5180.412-0.92940.296-0.0204-0.51830.4441-0.15250.4785-0.12250.05790.26040.00830.3286113.332696.5054108.0343
71.2408-0.1769-1.50710.8954-0.42438.9003-0.14590.3437-0.3663-0.04790.00270.01731.13210.15020.09670.30650.00090.01770.2768-0.14230.351485.828872.4323124.2734
84.21944.5398-3.94244.6977-4.29756.40250.0118-0.04660.06820.02120.02810.39780.005-0.11810.04050.2320.02010.02020.2262-0.07690.25981.845883.3989126.3383
94.2004-1.99221.72398.3272-4.14658.6197-0.10470.5866-0.3303-0.0242-0.05120.18140.1565-0.31570.17230.1524-0.04660.01110.3441-0.14840.311475.697376.6786122.8778
102.97881.36560.28874.14152.84976.1791-0.20030.5918-0.1856-0.17620.1080.20840.08640.19070.03710.13710.015-0.01330.3001-0.09820.225285.06980.1788121.9567
115.4406-2.3004-7.43142.26982.53322.0511-0.1596-0.3570.54850.18710.06690.01570.1041-0.0288-0.01370.22980.0215-0.0240.336-0.05680.254196.987176.1431107.5235
126.71455.87115.08078.76285.84124.3207-0.25490.37570.4256-0.66710.6363-0.6258-0.56180.7045-0.24710.3317-0.13370.11510.5143-0.20010.4694123.349490.7088110.8756
138.43422.52534.84251.54441.63965.57630.262-0.2438-0.29180.14730.0672-0.31980.19220.2671-0.32520.22410.0321-0.00460.2219-0.08230.2672114.869179.5792114.886
142.25062.40681.55463.84112.04562.7446-0.03730.2408-0.1555-0.02410.4299-0.6434-0.01620.4906-0.22090.2201-0.00960.00950.2833-0.09730.3127117.541980.8374110.9929
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'G' and (resid 45 through 73 )G0
2X-RAY DIFFRACTION2chain 'G' and (resid 74 through 258 )G0
3X-RAY DIFFRACTION3chain 'G' and (resid 259 through 475 )G0
4X-RAY DIFFRACTION4chain 'G' and (resid 476 through 492 )G0
5X-RAY DIFFRACTION5chain 'H' and (resid 2 through 119 )H0
6X-RAY DIFFRACTION6chain 'H' and (resid 120 through 215 )H0
7X-RAY DIFFRACTION7chain 'L' and (resid 1 through 29 )L0
8X-RAY DIFFRACTION8chain 'L' and (resid 30 through 48 )L0
9X-RAY DIFFRACTION9chain 'L' and (resid 49 through 75 )L0
10X-RAY DIFFRACTION10chain 'L' and (resid 76 through 102 )L0
11X-RAY DIFFRACTION11chain 'L' and (resid 103 through 113 )L0
12X-RAY DIFFRACTION12chain 'L' and (resid 114 through 128 )L0
13X-RAY DIFFRACTION13chain 'L' and (resid 129 through 163 )L0
14X-RAY DIFFRACTION14chain 'L' and (resid 164 through 214 )L0

+
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